This is kind of an unorthodox question.
I'm kinda new to using IDA Pro.
Is there a way to edit the assembly code and then have IDA save the result as an executable?
Is there some kind of plugin maybe that does that? because it seems that IDA doesn't want to save as an EXE.
Or do I need to manually edit it in some other way?
Version 6.1+ (maybe 6.2+) of IDA Pro will allow you to apply your patches directly to the input file. Equally, it allows you to revert the changes back.
I've seen somewhere else that you'd have to produce a .diff file from there then open with a text editor and use another program to patch the original file.