I have only done this once, it works if you are able to use a high, rounded shape. I filled the pan pretty full (about 3/4 or even 7/8 full) and made sure the oven was hot, so they ended up with a higher, rounded top. Then I sliced off the tops right at the edge of the paper liners, scooped out a ball of cake and placed filling in the hole. I glued the tops back on with bc frosting, then frosted/decorated them. This allowed me to put a larger amount of filling in them, and it still left the tops looking smooth and unblemished.
An easy filling for vanilla cupcakes? Light whipped ganache from TCB would be great, or I use strawberry puree (from TCB) firmed with a little gelatin. Because the cupcake won’t be sliced like a layer cake, it doesn’t matter so much if a little of the puree “bleeds” into the cake. It gives the flavor of fresh berries and isn’t too sweet.