If I want to form bigger branches of added cultivar on my multi-grafted tree, I usually graft lower and the tree tries to replace the size of branch that it lost to cutting and your graft would tend to grow to that size quickly too. If I want just add a specimen sample fruits I graft near the terminal sprouts, and the added cultivars remain small but are bearing few fruits of normal size. So basically you have some control on the size of the added cultivars by selecting where to graft.
One of the techniques of balancing the tree for me is instead of pruning I do the regrafting. Sometimes, in a multi-grafted tree, some added cultivars would want to take over while the others would remain small. So what I do, I regraft the more vigorous ones to the lethargic ones and lethargic cultivars I regraft over the vigorous ones. Somehow, after two seasons of regarfting, the tree balance is achieved and their growth almost the same.