Get your overall target based on how much water you're using to mash and top-off with. Add salts to the mash to get your pH in order. Then add the remainder (target amount - mash amount) into the boil. The idea is that since you'd be topping off, by the boil you've added your target amount of salts for 5.5gal into the fermenter.
Ions above what your target is (before diluting with top-off water) in the kettle should have no adverse affects.
~~ Malted barley wants to become beer. ~~