you could drill & tap the manifold now, and T it like you said. No problem. Heck, that's how I run mine all the time: single cooling line feeding both manifold inlets. (My second cooling line feeds the B-pipe.)
Just do it in a way so that both legs of the T are equal length-ish and that the lines hang as best as possible so air doesn't get trapped. You want the water to push the air up and through and out.
Just to make sure I know what you mean when you say "flow control valve", I'm gonna explain both things since sometimes the term gets misused:
- if you mean the spring-loaded ball assembly sold by Jetworks used to limit water flow to the stinger at idle, then you don't ever need one. It's gives a bit of performance gain (better immediate response off idle since the exhaust doesn't have to push water out of the waterbox first). Plenty of people run a B pipe and have no clue what a jetworks flow control valve is.
- if you mean an adjustable needle valve (technically also a flow control valve), where you pinch the water flow manually using an adjustable screw & lock nut so as to control the amount of water going through the overboard pisser, then you don't need one of those either. But you do want to throttle down the water flow that is pissing overboard somehow. Some people drill out old carb jets and stick those in the line at the pisser, I use nylon stand-offs from the bins at home depot. This restriction helps to a) build and maintain pressure in the B-pipe, so that it's internal bleed holes work more effectively and b) helps to dial in proper cylinder head temperature.
Hope that helps...