There currently isn't any facility for game saves, no. My rationale for this at the time was that PQ93 is quite simple, and most games made with it will be simple enough not to need saves. However, even the simplest games have a hi-score screen traditionally, so I may need to rethink this.
It is possible to create "multicarts", as described in the manual: the 'merge' function allows you to load graphics, maps, etc. from another cart. However, there is currently *not* a way to split your code among multiple files (real or simulated).
You can edit your cartridge with any text editor, which helps somewhat with the "huge file in a crappy editor" problem.