it wont stop circulation, but it WILL cause issues
because the thermostat is at the bottom of the system, the correct way to fill a Subaru cooling system is to raise the front end, fill the block thru the upper radiator hose, then attach the hose to the radiator, and fill it. This eliminates possible air pockets above the thermostat.
once filled, make sure to fill the overflow to the correct level, and put the rad cap on. then run the car to operating temp..
there is a bleeder screw (plastic) on the opposite side of the radiator from the cap, near where the upper hose attaches, that is the correct place for bleeding off any possible air.. not thru the cap. cap should be on to build the correct pressure for proper flow.
when you think you have it filled properly, make sure the overflow is still at the correct level, and check it religiously over the next week or two to maintain the level.
as for the timing belt.. definitely find the service manual for the vehicle your motor came from and check tooth counts.. they typically list two.. one from left cam (as facing engine) to crank, and from crank to right cam.. the crank to right cam is very often given as xx.5 - meaning half a tooth..
most service manuals can be found here: http://jdmfsm.info/Auto/Japan/Subaru/