Cowl area cleaned up.

I would carefully fit the bottom piece to the car, weld it in, then fit the top piece to it.
Remember, the top of the cowl has to align perfectly with the top of the fenders. Fenders should be aligned temporarily before fitting the top of the cowl.

Might be better to get core support and inner fenders in place prior to fitting cowl top so you can be sure height is correct.

If it was me I would have everything clamped in place and test fit fenders before I would weld anything.  I installed both the upper and lower cowl panels from NPD.  What I found on my car was they fit right in place and I did not have to try and move them around.  Not sure you will need to hammer anything.  Just clamp it all down and weld.  I would also install them in separate pieces, not together.    I also test fit the wiper motor and arms.   They pop through the openings but are a little off center.   

I replace the battery apron and core support. Even though the top of the core was dead on with my measurements I found the aftermarket apron was pushing the center outward.  This was with the top and bottom of the core support being right where the factory one was.  This area being pushed out could cause fitment issues the front valance parts.   Just something to keep in mind.