Actually, the covering always moves the CG back, for two reasons. First, the tail is about twice as long as the nose, and second, there's a lot more material back there to cover the rudder and stab. A kit usually has things worked out well enough that you'll be safe installing pushrods and covering and doing final balance with radio position. If you're scratchbuilding, it always pays to check balance as you go. You have to be able to make it just a little nose heavy without covering. If it's coming out too nose heavy you can do things like building a (robust) batterey box behind the wing compartment or moving servos to the rear of the plane. If it's coming out too tail heavy you probably need to do more sanding!
Regarding the Somethin' Extra....almost everyone ends up moving the balance point back after the first few flights, sometimes a lot, but because of that 2:1 tail-to-nose ratio, it doesn't take a whole lot of lead to make a significant move, so I wouldn't worry about it too much. I bolted two chunks of 1/8" lead about 1" square to the bottom of the rudder right behind the hinge line to get mine where I liked it.