Need handholding -- can't make formatting pretty

[MeiraV]

Hi!

Complete newbie here, sorry if my ineptitude is annoying!

I downloaded Calibre a couple weeks ago, very excited to be able to convert all these ebooks to epub for my iPad. The first bunch I tried were PDF and looked pretty bad. Did some research on Calibre's page and found PDF was one of the worst to attempt to convert. (Ok, fine. I'll use GoodReader for them.) Also found that .lit were the preferred format. Got an account with whomever to get pretty metadata. Tried to convert some files, nothing worked well enough, gave up and went to Amazon to buy a fresh copy. Today I attempted to convert another .lit file and the formatting is such that "page x of xxx" is breaking most of the paragraphs and then the author's name/book title is thrown in every 200 words or so. Tried it again asking Calibre to remove headers and footers, turned out exactly the same. Technically, it IS readable, but I want it PRETTY. Perused the Calibre manual but the cure did not jump out at me.