You'll need to use a pulse extender. While I can't be perfectly sure how, since I don't know exactly what you're doing, I can give you an example on how to use one. Here I have a simple piston circuit:
When you flick the lever, it moves the dirt block up:
The magic occurs when you flip the lever back down. The dirt will return to its original position, and the pistons sync up. The way it works is simple. It makes the bottom (pushing up) piston delayed a little, and it makes the side piston start quickly but stay on longer when you turn it off.
The repeater leading to the bottom piston is straightforward, it will just delay the piston a few ticks to wait for the other piston. The other set it slightly more complex:
The set of two repeaters is what actually extends the pulse. The 1-tick repeater goes through quickly, so the piston will turn on quickly. The 4-tick repeater goes through takes more time, so it will keep the piston on after the lever is turned off, and the piston will retract more slowly.
The third repeater in this image is simply there to prevent a small Minecraft bug. If you take it out, the piston will quickly retract and push out again when the 4-tick piston is powered, even though the wire is still powered correctly. Placing an additional repeater stabilizes this signal, keeping the piston extended.