Regarding fixing things together I wasn't sure which approach either, so I'm doing them all!

Using bolts where they will fit and screws everywhere else (lots and lots of screws). The HDPE I have doesn't take a thread very well, and I was worried that if I kept inserting and removing screws for maintenance they would get loose so I have a hinged trapdoor for access, going to try the inserts route for sealing it.