I know that "transcoding" is very bad when talking about lossy to lossy formats... but is it ok to convert my FLAC files to WMA or do I need to convert to the FLAC's into WAV's first, and then to WMA? Please Help

Assuming that you don't have any software issues, encoding from FLAC to WMA would yield the exact same quality as directly ripping the CD to WMA or encoding the FLAC to WAV and then the WAV to WMA.

It's OK to convert from lossless to lossy, and depending of the software that you use for such task, it's preferable to convert from FLAC to WMA directly, instead of using WAV as a middle step, because you'll preserve the original tags (they will be copied from the FLAC files and written into the new WMA tags). But that's depending of the app you're using, foobar2000 does this for example, others may do not. Besides, it's faster

Thank You guys... I will now start the process of converting my 4000+ FLAC files... arg.

If I may ask, why are you converting to WMA as opposed to some other lossy format?

WMA cause that's what my car supports... well, that and mp3... but WMA is smaller size so I use 128kbps.

At 128 kbps, listening tests seem to show that mp3 is at least as good as wma, if not better. If you were encoding at a lower bitrate then wma might have an advantage.

Since you are transcoding 4000+ files and your car player supports both MP3 and WMA, I'd go with MP3 @ 128kbps.

With the high inherent ambient noise in a car, I doubt you would be able to notice any difference between MP3 and WMA @ 128kbps VBR.