Sometimes my meat pies do not cook properly on the bottom. I usually put the filling in cold rather than hot. Should I cook the bottom pastry blind before adding filling and top.
There are two techniques (that I know of) that will help you. I often use both...
I don't know if this helps with 'cooking properly' or not, but I use vodka to replace half of the water to mix the dough. This inhibits the production of gluten and makes a 'flakier' crust. (based on a tip from Alton Brown specifically for apple pie, but it works all around...)