The drive you rip from does not really matter.
Use EAC for a bit perfect extraction and watch the log for errors. I use the test and copy mode. The Accurip database will tell you if your rip matches others. The higher the match the more you can be certain it is bit perfect.
Rip your CDs to either wav files or flac. Personally I compress my files to flac. I also create a cue and sfv file. With 3000 CDs you want to do this right the first time. I personally do not like AAC files.
You can have files on more than one drive. I create 2% par files in case a file becomes corrupt. I also use an online backup service. I also have a few thousand CDs.