Bundling and Updating Files

I'm trying to figure out how to make Calibre work for my needs.

One problem is when I have several html files I want to keep together. I used to convert to epub files. I still need to convert to epub files for compatibility with my e-reader, but it is a pain and a half. Is it possible to bundle files together, to convertt the bundle to one epub, etc.?

One more problem is if another installment arrives, or if I need to replace a corrupt or unreadable file with a better copy. Is it possible to do this?