Non-canon shouldn't be an issue if you can cover your quaters. For example, I have a completely new race which begs the question "Well, how come we never see or hear of these in the Star Wars franchise ever?"
So I made their home planet get destroyed by a natural disaster and had them leave for new territory. It is very likely they would avoid contested ground at all costs, as they could be attacked by either side. If the Clone Wars was going on at this time, few inhabitable areas would be neutral. Even after they ended, there would still be a lot of hostility and potential revolts. So, after the collapse of the Empire, they found a somewhat empty, peaceful sector to settle down in. Some people might say "Well, why didn't we here about the Jedi/Sith Ke'ter who wouldn't need to look for a new home?", but I covered that problem by saying there were no Jedi/Sith Ke'ter.
Therefore, as long as you can justify any non-canon, there really shouldn't be a problem. Take anything that's non-canon and say to yourself "What changes would this have on the canon universe?". If the answer is "Not many" then you should be fine.