I was planning on painting a coat of primer on the engine compartment firewall and it occurred to me that the seams have not been sealed yet. My question is do you apply seam sealer first or can it be done after it has been primed? 

personally .. I painted first .. then seam sealed.. then top coated the paint again.. overkill I'm sure.. but there will be no rust starting under the seam sealer / bare metal in my mind that way.

quality seam sealer is meant to be top coated .

I'd agree with prime, then some colour into the clean seam. Only then the sealer and topcoat. I've heard that that seam will probably flex a little. So too much paint on top might crack.

But the best thing you have going for you...the seam has no rust! Nice!

I just went through this recently. I agree. I used some rustkiller primer then seam sealed. Then will prime again then some color.