I would flush it before you put the new rad in, get some flush stuff(stuff I used last time worked great, it was a powder from Prestone I think, worked better than the liquid stuff, took ALOT of flushing to get the crap out of the 45 wagon 350 and rad)
if you flush and fill, flush and fill, ect ect like the directions tell you it will take all day and crap and nasty colored chit will still be coming out.
Heres what I have been doing, after the 1st flush(noramaly you run the motor with the flushing stuff for a hour or drive for a while, do whatever it says on the can) Let it cool down.
Drain from rad and block.
Leave drains open. then stuff a hose in the top of the rad(Ihave the flexible rubber nozel that works great, it only runs when bent) let it run keeping the water just level with the top of the rad(so it doesn't run out and doesn't spash everwhere) and untill water comes out the block drain. Then start the motor and let it idel. let it run like this untill the water runs clear(making sure you don;t run out of water), at some point close the rad drain but leave the block drain open. Use a pan(s) so you can see the crap that comes out.
Works pretty darn well, I can leave a rig run like this while doing other stuff, if the pans overflow it;s just water(by this point) coming out anyway.
Better to do it before the new rad is in if possible I would think.
John H