For the multi file result from lit, it can be easily merged with free software; or you can use AmberLit to make one file, though it may lose stuff doing so (footnotes and the like).
Also with MobiPocket creator you can use the opf file from the lit conversion and make a prc book which preserves the structure and is more useful in general
Personally for Pc reading I prefer Firefox for a quick look around and see if I want to bother and Mobipocket for more serious reading.
For storing, well you cannot go wrong with html and multiple backups (blank dvd's are cheap, and e-books do not take much space especially if you zip them, so you can backup in 2-3 formats or more just to be safe)
I tried both uBook and MsLit, but overall Mobipocket for text-based e-books and pdf's for technical stuff work best for me on a Pc or tablet, with your favorite browser as a quick look around