Any Suggestions for EPG

I have my m3u all set up but all of the channels are not available in the same epg source. I us xmltv to get my EPG's. Can you use more than one epg on channels?

No.
You will have to split up the m3u and xmltv into separate sources.

Or follow the advise of a Channels developer here

If I do seperate sources, will it still recognize the 2 sources when I import into threadfin for Plex?

Not sure, I don't use either one.

Threadfin when imported into Plex will always show only 1 source it will combine them ... if you want several sources you have to run a 2nd instance of Threadfin with a different port and config.