Um... how about you treat it like a drug... just say no??

"DoOm dOoM DOOM!"

are you singing Gir's Doom Song now???

I'm doing magical time travel... which basically means I get to make up the rules. :D

Well, if you make your own rules, you pretty much bend them according to what you need in the story. You probably don't even have to decide if you want to go with the idea that there's only one universe that changes according to what happens in the past, or if you want to go with the idea that for each possible change in the past there's a separate (parallel) universe that reflects it. How crucial is the time travel to your story, anyway? If it's only of secondary importance, you could theoretically get away with it without killing your brain with questions like 'what if', and 'when', and 'then what.'
But yeah - doom is upon you. ;)