Hey I am currently doing a run that has save points in between the story chapters, am I allowed to submit a run that is in segments but put together in one video?

You would have to make it clear that it is a segmented video.

Single-segment is the whole way through, not stopping from start to finish. You are allowed to save during that time, but usually saving is adding time to the counter while it goes through the process.

If you are saving, and then completing a section to it's best time, and then stitching all those multiple runs together to make it looks like it's a complete run, then that is a segmented run, and must be made clear.

What game are you running?

EDIT: Saw the post just below about South Park 64. If you want to do races, or widely have it accepted without issue you can only use some older versions of the Project 64 emulator.

I don't know if the rules have changed (http://www.speedrunslive.com/faq/rules/), but you should only be running Project 64 1.6/1.7 not version 2+, since it doesn't emulate accurately.

Thanks for the info. And I am not running the South Park, that is a later project. I am currently running Custom Robo for the N64 and decided I will just do a single-segment to make it easier