Measure and re-measure before drilling.
If it's a runabout do a dry fit and make sure the center window will clear the tower legs while opening/closing.
I like to put the back part together too and hold it up to the boat so you can make sure it folds into the boat the way you want it to.
After you mark your holes make sure there's nothing behind where you will be drilling.
The above advise is good too.