I'm currently trying to backup my CDs into FLAC. Many sites recommend that you make WAV files with EAC and then encode them into FLAC. However I noticed that you can open the CD with foobar and convert it directly to FLAC there. Is this inadvisable? I also have some APE files that I want to convert to FLAC. Should I convert APE files directly to FLAC with foobar or should I make it into WAV files before converting it to FLAC?

It doesn't matter.

Also, pretty much every method converts to wav at some point since most lossless encoders can only take wav as an input. Many just do not store the wav after they've done the lossless compression.