Hey all, is it better to lap and spot weld the seam or butt weld the pieces where the floor pan meets the drive train tunnel? I think this may be important before I start cutting. 
Assume you mean floor replacement panels to tunnel, right? Original floor/tunnel was one piece. butt welding is the best way if you have the skills, butt welding can be difficult, i.e., to not blow through.
If you have replaced a partial pan before…try seam welding, if not, lap weld it. Because you don’t want big gaps that are impossible to fill. Doing seams take time. And a lot of test fitting.
I agree with Bob. Butt welding the joints is the best way to go if you have a good tight joint. If so then it’s a lot of spot welds and patients. Eastwood make a magnetic level guide that can help greatly with this type of work when adjusting the seams at the area to be butt welded.
Steven
Like Bob said, butt welding is the best method but is the hardest. Cut your piece about a quarter big and clamp it in place. Use a sharp ice pick of sorts and scribe your metal. Remove it, trim however you do but leave that scribed line. Then fit, grind, fit, grind until its almost a perfect fit. And your ready to weld.
Take your time, make sure you can see what your doing through the welding lens (I finally bought a digital hood and thats the only way to go) and have an air source to cool each weld right after you make it. If you cool each weld the panel will not continue to heat up as you go and you will not have warpage.
Practice on a piece or too first, of course.
Have Fun!
What some people do is make the panel big (as ccarney mentioned) and lay up the panel, but then use a air body saw to cut through both the new panel and the existing one, this makes the new panel edge follow the old metal edge exactly (and with an air body saw leaves only maybe 1/32" gap from the blade thickness). For doing (for instance) quarter panel patching on a high dollar car, this is the way to make a job that is undetectable after the work is done (from say inside the trunk). Can’t say I would be excited about trying to do it, but then I have not had need to either (with a non-rare car such as Isabel). For ccarney, he might want to try this in some spots given that he has a rare car.
Butt weld is the way to go. If you’re really pickey you can always wipe a bit of body filler on the underside of the car after welding/grinding to give the perfect seamless look. This is how the driver floor was replaced in my Cougar. We used a sharpie and then cut/fit about a half dozen times. These little guys helped spacing and aligning for the welding process. Taking your time is key.
THANK YOU for all the suggestions yall, OK, I have successfully butt welded my floor pans in and am wondering what to coat them with after grinding? do I lay seam sealer over bare metal or should I prime it then seal it?
Thanks again for the replies. I have primed all the ground bare welds with rust encapsulator and then swiped seam sealer over them on the inside of the car. This will be covered by dynamat anyway. Underside I just primed and did undercoating on the entire bottom of the car. Can barely even see them.All is good. 