Here's the simple step-by-step guide to making flawless filled cupcakes. This easy technique can be used for any type of filling, so feel free to experiment!
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Remove The Centers
Insert the base of a large pastry tip (I use Ateco's #800) into the center of the cupcake about 1/4 inch deep (1/2 inch deep if filling and then frosting), and twist until the cake center twists alongside the tip; pull directly up to remove the center. Reserve the cake centers if your cupcakes will be frosted (rather than just filled), otherwise discard or eat the centers.Dust With Powdered Sugar
If dusting the cupcakes with powdered sugar, do it now, as otherwise you'll coat the filling with powdered sugar. Spoon about a tablespoon of powdered sugar into a fine mesh strainer and sift it over the cupcake tops.Fill The Pastry Bag
Nestle a disposable pastry bag (or large resealable bag) in a pint glass, folding the top half over the glass rim (this helps keep things tidy). Spoon in the filling until it reaches the glass's brim; firmly tap the glass on the counter to settle the pastry bag's contents.
Now, pipe in the filling using a pastry bag, and if you plan to frost the cupcakes after you fill them, leave about 1/4-inch of headroom, slice off all but the top 1/4-inch of the reserved cupcake centers, and then place them on top of the filled centers so that they're flush with the top of the cupcakes. Then pipe the frosting.
Finished!
The filling will seep into the cake, so fill the cupcakes right before you plan to serve them, at most 3 to 4 hours before eating.
Happy Baking & Enjoy!
Article Source: Delish

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I just make dollops of the filling then freeze it. Put them in before baking. Viola.