I have a 98 12v with a #6 plate I just installed a after market tc and when it goes into lockup with a heavy load I here a wopa-wopa noise from the turbo is this a bad thing, if so what can be done.

 

That is called "barking the turbo" or "turbo bark". Mine does the same thing. The only way I know to stop it is when it it is going to shift into O/D is to let off the throttle. I don't have an explanation though.
Tom

 

It's back pressure on the turbo compressor blades...from a reduction in power (rpm). Usually happens going into OD to early. Not good to do very often. You can accelerate through it also. You can learn to drive around it...big thing is try never to back off throttle too quickly....is caused by rapid reduction of boost.

List your truck details under USER CP-Signature, so we know more about your truck and can give better answers!

RJ