I had the same problem when I installed my Pioneer TS-A6995'* last year. I'm assuming that you mean that the black plastic bracket that holds the stock speaker in place doesn't fit your new speakers?
In my case, the Pioneers were a little too big, so all I did was take a utility knife and start carving away the opening of the bracket until it did fit. The plastic is fairly soft, so you shouldn't have a problem if you have a sturdy enough knife, I don't recommend an exacto knife since they're kinda flimsy and you'll dull the blade very fast. If you can get a proper utility knife, trimming away the excess plastic should be no problem.