This and the rest of an alignment you CAN do with the pans on.

I leave the pans off when I am doing any real work on the car, but I always put them back on for any long trips. Saved me from engine damage a few times from some serious road debris. The plastic one was sacrificed three times, deflecting the debris (18" long drilling rig pipe in one case) back down under the car where it did less than fatal damage.

 

I lost an AC compressor because I didn't have the pan on once. Another time I saved my AC compressor because I had it on.

I follow Bills thoughts on this. I take it off, but I try to put it on for any serious trips.

 

While it can be discouraging being faced with the chore of removing the belly pans yet again. An hour's effort to renew all the fxing screws with stainless roof sheet self tappers (one size up from stock) and matching size speednuts makes removal easy and when replaced all is much more secure. The only place this doesn't work is the attachements to the frame rails for the front end of the rear pan. M6 rivnuts are the solution here.

 

Those front 'ears' on the original pan suffered to failure on my car. Plus I wanted to bring the front edge up half an inch along with the trailing edge of the front spoiler. So I made a front brace that attaches at the frame (using those same M6 NutSerts) and follows the same original contour, less half an inch, that the original pan brackets and pan formed. More NutSerts in the bracket where the pan screws hold the front edge. Originally these were screwed into little spring steel tabs brackets that hang on the radiator sheet. So five machine screws across the front, the original two in the NACA ducts for motor mount cooling, the two 6mm bolts into the rack (now with stainless fender washers with foam face added), plus three that connect the front pan to the rear pan. Net effect is that the front pan comes off and goes back on in just a few minutes.

Harbor Freight sells cute little magnetic parts trays, in several sizes. The 4" round one is particularly suited to holding the stray bits and hardware for the pan. Often on sale for $1, they also keep lug nuts in one place, and are very handy under the hood for keeping hardware organized. They come in 6" size also, and there's a larger rectangular one that's great for holding small tools. Except for the aluminum lug nuts which end up sitting on the lift arm in the tray anyway, bumping a tray doesn't scatter parts and tools around.