I have no clue if WMM accepts DirectShow-based input, but if it does, then you need to install ffdshow and Haali's Media Splitter.
ffdshow (the newest version is the one at the bottom of the listing):
http://sourceforge.net/project/showfiles.php?group_id=173941&package_id=199416&release_id=439904
Haali's Media Splitter (the link says 'Matroska Splitter' - it's in the upper right corner):
http://haali.cs.msu.ru/mkv/
The splitter will allow parsing of MOV files, and since most MOV files these days contain H.264 video streams and AAC audio streams, ffdshow will act as the decoder for those. This solution will allow you to play MOV files in Windows Media Player, and anything else that uses DirectShow.
I will now explain what some of those settings are, as those are fundamental properties of digital video, not just something exclusive to WMM. Be aware that some of this will get kind of technical.
Bitrate is more or less a measure of quality - the more bitrate a video or audio file has, the more quality it has, generally speaking (the old garbage-in, garbage-out idiom applies here, in that if the source looks bad all the bitrate in the world won't do a thing for it, but high bitrate can preserve any quality that exists better than lower values can). Bitrate also directly ties into filesize - because the bitrate is usually measured in kilo
bits-per-second, or kbps, and if you divide that number by 8 you get the value in kilo
bytes-per-second, which means X amount of kilobytes per each seconds in the video (and of course, 1000 KB = 1 MB), so multiply the KB value by the total number of seconds and you have pretty much what the output size will be, as long as the bitrate stays constant and doesn't fluctuate. Generally speaking, a bitrate of 1150kbps makes a file that takes up 10MB per minute of video in size. So, depending on how small you want to make your output file, you can figure it out that way (there are also dozens of different bitrate calculators available online that can perform roughly the same math).
Framerate is more of an issue if you're trying to author something for hardware-based solutions like DVD or whatnot. The rule of thumb is that it's best to keep the framerate the same as the source, although depending on what WMM's profiles are, this can be an issue (if say, the MOV is 60 frames-per-second, WMM's profiles may not allow that - not that 60fps videos are at all common yet, but they do occur). If you normally use VLC Player or even Quicktime Player, then you can view the properties of the MOV file and this will tell you the framerate you need to shoot for.
Warning: Aspect ratio is more complicated of a concept to grasp - in short, it refers to the number of pixels wide by number of pixels tall (16:9 is 16 pixels wide to every 9 pixels tall, 4:3 is 4 pixels wide to every 3 pixels tall)
Aspect Ratio (I'm assuming this is not aspect ratio as much as it is aspect ratio
flagging) means the way the video is shaped - 16:9 widescreen, 4:3 fullscreen, etc. Most video distributed online fits one of these categories, but most of the time, the video's pixels would be described as having a 1:1 ratio, or having 'square' pixels. PC monitors have square pixels, which is why this is the case for most online video. Televisions (at least, of the non-HDTV variety) have pixels taller than they are wide, which is why there's a need for flagging a ratio (this would probably apply very much to stuff recorded on a DV camcorder moreso than average PC pixel ratios would). I'll explain this a tad later.
The pixel ratio doesn't affect whether the video as a whole is widescreen or not, but it does affect something known as anamorphic video (on DVDs anamorphic video is recognized by things such as 'Enhanced for 16:9 TVs' or more directly 'Anamorphic widescreen'). Basically it means the video is technically in one resolution to optimize how it's stored on disc or encoded for distribution, but it has a data flag which the decoder/hardware player will interpret and resize the video correctly so that it still looks right to the human eye. On DVD,
all video is stored at a resolution of 720 pixels wide by 480 pixels tall (or 576 pixels tall if the DVD is from an area other than North America or Japan). What the flags do, depending on what aspect ratio is specified, are dynamically resize the video on playback so that it displays as roughly 640x480 (in the case of 4:3 flags - this would even apply for older releases of widescreen movies which employ hard letterboxing), or 848x480 (in the case of 16:9 - movies with wider ratios than 16:9 are hard letterboxed but still use the 848x480 resizing, because they're only letterboxed to make them fit into a 16:9 ratio instead of a 4:3 one).
Basically, if you're dealing with HD source (whether that's 720p or 1080p), then you'll always want to choose 16:9; if you're dealing with the output from a non-widescreen camcorder, you'll want to choose 4:3. Now, the tricky part is in how WMM would see this - generally, I would assume that if you choose that option it would resize to 720x480 or other corresponding 3:2 ratio before applying the flag, but it's possible that it's more involved than that. The tell-tale sign of a wrong aspect ratio is that the people or objects in the video will either look too tall or too fat. Having something onscreen that you know to be a definite circle and seeing whether it looks more like an oval is a common technique to determine whether the aspect ratio is correct (if it's correct, a circle will look like a circle).
Something you didn't mention was an option for interlaced vs. progressive video - this can make a big difference in perceived quality. Interlacing is the method of breaking up each frame into even and odd lines and transmitting them at slightly different times - it cut down on bandwidth concerns in the early days of TV broadcasting, and can be seen visually on a computer because it leaves nasty horizontal lines through the video that appear notably when something moves. Progressive video transmits the entire frame at one time and thus doesn't have those nasty lines sticking around unless something went horribly wrong in the conversion stage. If you see those lines in the MOV file, you'll want to look to see if you can find an option to 'De-interlace' or 'match fields' (these will keep the video at 30fps) or alternately, to perform an 'inverse telecine' (aka IVTC; it matches the fields to each other and then removes the duplicates to restore a framerate of 24fps, which is the standard for Film). If the video is already Progressive, make sure that those options aren't selected and that the encoder knows you're working with Progressive video (if an option for 'Top field first', 'Bottom field first', or 'Interlaced' is selected, uncheck it).
As a note, I don't use WMM nor do I use WMV at all - I rely either on Xvid AVI files or H.264 MP4s or H.264 MKVs. I do this using a combination of programs, including AviSynth (which is a scripting language) and either VirtualDub (for Xvid) or MeGUI (for Xvid if I need the computer to shut down when it's finished encoding, and H.264).
