I think it depends on the size of the connectors. I'm getting ready to do the same thing and mine are 3x2" square steel tubing. I'm thinking I'll have to cut the floor right behind the seat mounts and before the shelf for the back seat. Check the tech section of you haven't yet, good info.
You can do it both ways and add a lot of stiffness to the car. Notching them inti the floor and welding the floor to them is the strongest way. On my Duster I put them in the floor, but in my Valiant I didn't want them in the floor so I notched them to follow the floor.
I used 2 x 2 stock for mine (72 duster) and they came through the floor but only about 1/4". Can't tell with the carpet in. Having them come through the floor and welding them up will GREATLY increase the stiffening of the structure. Do it.
I did mine per the tech pages with the long side horizontal. You have to cut the floors and the tube sticks up about 3/8". The carpet will hide that. I welded mine up solid.
Cut the tube steel, slide it over the rear sub frame and hole it tight to the floor with a jack. Scribe your mark, take the tube out and cut it with a .045" cutting wheel. Cut a little at first. You can always cut more later if you need to.
not to steal the thread, but what is the deal with having the car resting on its suspension when you weld them in? jackstands under the front and rear subframe won't work? With the car on its suspension there is no way I can get under there to weld.
Using the measurements and steel tubing from Tech Tips...will you need to notch the floor pan??? The reason that I ask...is that I like the idea of notching the pan and welding it to the pan. It seems to me that by doing it this way it really makes it more rigid.
My son's Dart is going to be running a 383 and 4 speed...so twist needs to be addressed...