Will completing the dark brotherhood questline effect my experience with the main quest at all? Will I be killing anyone that I need for the main quest? I read somewhere to do the main quest first, but I'm not sure. Can anyone confirm?

It doesn't in any way affect the main quest. Nothing you do in the DB quest line changes anything in the main quest.

Any character that is necessary for the completion of the main quest cannot be killed, so you needn't worry.

Alright, thanks