I just got my new motor guide that i ordered last week... I cant wait to use it, it looks sweet. When i go to mount it should i fill the old holes in the boat from my old trolling motor with something? If so, what?

It's not necessary to fill them.  If you're lucky they will match up.  If you need to there are a bunch of fill bonders you can use.

If the base of the new motor covers them up, don't worry about them.  As mentioned, I would try to reuse any that might fit.  

A couple of hints I will pass on.  I would not spend the money for those TM bounting bolts that requires you to drill a huge hole for each one and have the rubber base that compresses into that huge hole.  I've never had a set of those hold up, and the motor is constantly getting loose.  

I drill 1/4" holes and use 1/4" brass or stainless bolts with self locking stainless nuts and washers on the under side.

Make sure the base is level/squared off on the mounting surface, this usually requires using stainless washers as shims between the mount and the boat.  If it's not level and one corner pulls down more than the others, even just a little, it can make getting it to release a real pain or you will have to pull extra hard on the rope to get it too release.