FBReader n00b

[jupider]

First off, greetings everyone. I'm new here and I created an account solely for posting this question, but hopefully I'll find a new hobby in eBooks and stay. In any event, here is my situation:

A friend of mine has about 4gb worth of compressed (.zip) files of .mobi formatted eBooks. Thousands of them. Don't know where he got them, I don't care and that's not the point. I grabbed a handful of them (only had a 1gb flash drive on me at the time. sigh.) and copied them onto my ASUS Transformer TF300T tablet. The Kindle app nor the "My Library" app that comes pre-loaded on the tablet could apparently find or see the compressed files, so I unzipped them into an /eBooks folder I created on my tablet's 8gb MicroSD card (NOT the internal storage). Well, Kindle and "My Library" *still* couldn't find them because I guess any books for those particular apps must be in a particular directory in internal storage, and since I don't want these books eating up all my internal storage, I found FBReader in the Play Store which could be configured to look for eBooks in a custom directory. I did this; configured it to look for the books on the MicroSD card. Well, it found them all, but the problem is, it found *two* of each book. As it turns out, there is a .mobi *and* an .opf file in each zip file, the former of which is the actual book and the latter simply an apparent "metadata" file that stores additional information about the book.
Well, I didn't want my list to be populated with two of every single one of these books, so I pulled the MicroSD, plugged it into my laptop, and deleted all of the .opf files, since they are apparently not necessary anyway. Problem is, without the .opf files, all the information about which books are in which series and in which order was lost.
Geez, I'm going on forever here... Here's my point: Is there a way to have both the .mobi AND .opf files on the MicroSD card, but only have ONE of each title appear in the list?
(I'm sorry if this is long-winded and convoluted. Feel free to let me know if anything needs to be clarified further.)

Thanks. :/