Most of your books are LIT, aren't they? I have never used Microsoft Reader, but it seems that the most popular program around here is
Book Designer, and it also converts LIT. Here you can find a good tutorial to get started:
https://www.mobileread.com/forums/showthread.php?t=10313 This is another program you might want to check out:
http://www.processtext.com/abclit.html
If you find any problem, don't hesitate to ask. People are very helpful around here.
PD: Except me.
But that's only because I know nothing.
I forgot to mention that you can use the Reader software (
http://ebooks.connect.com/downloadclient.html) to preview how your books will look on the Reader. This really comes in handy when you are formatting your first titles. You can also check if the links work, bookmark certain pages, or organize your books in collections. I don't find this last feature very useful when organizing all the books on my PC, but it makes it easier to find books on my Reader.