Most of the time, you either have a shorter rod or a piston with a shorter compression height, and by that I mean, the new pistons have the wrist pin located closer to the top, most of the time this causes issues with interference of the ring lands and wrist pin and eventually leads to burning oil and is not the preferred way of doing a stroker.
The preferred method is to build up the rod journal and then machine it down to move it farther out on the crank (farther from the center of it) then you take how much stroke you added, let's say .5" and you buy or make connecting rods that are .25" shorter, this will maintain your stock compression ratio and allow you to gain additional displacement.
Many times you can use connecting rods from another engine to fit the crank and pistons together rather than having to make new ones. Just like some ford 351w stroker kits use 302 pistons and rods or even some use Chrysler connecting rods, all you have to do is find something that fits.