There are drill attachments you can buy at Lowes/HD/Ace that will cut a hole in the metal. They are made for metal and they come in many sizes and for various metal thicknesses.

The best method is a hole saw for round holes.  Then use  a round file to smooth the edges.  

Big box stores, EBay and the internet have Bi-metalic hole saws available in many diameters. You will need a heavy duty, slow speed drill (double gearing) to run the larger bits.

Because you will be drilling different diameters for the different applications, it would be better purchasing an armature and the various cutting bits, rather than individual bits.

If you try to use a single geared drill, the high RPM will over heat the bit tips and burn them up. You will want to go slow and steady with a high torque and slow RPM. Depending upon where in the body work you're drilling, you may want to use some cutting oil for cooling on the thicker sections.

Should you drill separate holes thru the drop wall for water supply line and electric or is it okay to feed them thru the same hole?  I was curious as to any potential troubles using the same hole.

Also, any tricks for sealing that/those hole(s) around your lines?

You will want the holes to only be slightly larger than the items they will contain. Running both electric and water in the same hole will require a larger hole than is necessary for each. Also the electric line should be protected from the surrounding metal by grommets, clamps, and anti chafe looms. The water line, if flexible, can be protected by splitting another piece of the same tubing, and placing it around the areas most likely to chafe. If it is rigid, it must be protected in the same manner as the electric run.

If you use a good grade of caulking, it will easily seal the tight fitting gaps you created.