my centering skills are a little suspect,
For next time (or anyone else doing this type of task)...
Assuming you mean centering your new screw holes so they align with the speaker mounting holes, (as opposed to centering the speaker on the hole in the cabinet- also important, but can be done using measurements), this tool stays in my tool kit:
It's a Centering Punch Tool. That black tip is actually spring-loaded. You place the bottom tapered part onto the speaker mounting hole, and tap the top part (which would be sticking above the barrel, due to the spring inside, if the picture was accurate), with a hammer, which drives the pointed end down, and leaves a perfectly-centered imprint into whatever material you're going to screw into. It's best to use that small indent to then drill a pilot hole into, using a drill bit that's a bit smaller than the screw you're going to use.
I use that method/tool when installing new door hinges, since those screws need to be centered in the hinge holes.
As far as screws not being long enough (I run into this on occasion), sometimes you need to drill a larger, recessed hole, usually from the back side. I run into this problem when attaching door/drawer handles to kitchen cabinets, if the hardware doesn't come with a certain kind of (extra-long) screw, that the shaft can be broken off with pliers, to make it shorter.