Ah hah! And yeah I just found the filename thing on page 3 of the FAQ thread here. I wasn't sure I'd find it so quickly.
And d'oh

on my missing that system tray option. I must've gone past that several times in trying to find things in the configuration. (I'm still not sure on what a couple of them do, single file save for example, but I was going to finish reading the user guide before asking any more.) LOL
I suppose I should uncheck the "show notifications in system tray" as well? I don't know what that does differently as I haven't had any kind of notifications from the program.
Right now the problem I'm having is trying to force pagination. Like if a PDF file pages at a particular place, I want the resulting MOBI to paginate at that same place. I know that's probably discussed here somewhere though. (Feel free to point me to it if you know where it is though as searches are giving me way too many threads to look through.)
Thanks for the very useful program, and for the quick responses here too.