Ahh, the sheet metal.
If this is the only project your ever going to do investing in hole saws or chassis punches may not be cost efficient. You can cut nice holes with a jigsaw but it's more time consuming and limited to the minimum radius the blade is capable of, sheet thickness is a factor here. If you want a really neat hole, rough cut with a jig saw and finish to the line with a hand file. It's tough to get a perfect round hole with just a jig saw cut. Practice on scrap first before butchering that expensive panel.
Hole saws are cheaper and more versatile than chassis punches but leave a rougher edge that has to be finished, but are a lot faster than a jig saw. They sometimes wobble a bit and consequently cut the hole bigger than the actual measured size. Always practice on a piece of scrap before making that first cut if you haven't used them before.
Jig saws should be duct taped on the bottom plate to keep from scratching the aluminum, and it scratches easily. You can also duct tape clamp contact pads. I've even taped the edge of the metal bench to keep from scratching when dragging sheet across it.
If your jig sawing to an inside corner always drill a hole first right at the corner and then carefully saw to the hole. Sawing all the way to the corner can leave a notch that's hard to finish out and leaves a stress riser which causes cracks. Thin sheet should have at least a 1/16" inch (1.5 mm) radius on inside corners, so minimum 1/8" drill, and 1/4" is better.
It's not absolutely necessary for a minimum amount of cuts but you can lube the cut line with cutting oil. For a lot of cuts it makes your blades last a lot longer, keeps the teeth from clogging, and cuts smoother, although it is messy. Look for a clear cutting oil, anything else hides the marked cut line. For thicker aluminum plate in the hardened alloys cutting oil is almost mandatory. WD-40 and 3in1 are NOT cutting oil, although they will work in a pinch.
Always mark lines with a marker, not a metal scriber. Scriber's scratch the surface and cause stress risers which can eventually start a crack. You may be cutting on the scribe line but if you go a little past your cut with the scribe mark, or miss the line a little when you cut, you'll leave a scratch.
The only felt tip marker I've found that works best for metal is the Sharpie by Sanford, but it does get blunt pretty quickly unless your careful. You'd be surprised how many markers don't work well on metal.
Always measure twice and cut once, or measure 3 times and cut once depending on your cognitive capacity, how much sleep you got the night before, and the cost of the part. Sometimes I'll make notes on the metal with the marker, like, inside, outside, driver side, passenger side, in case orientation is a factor. You marked your hole in exactly the right place, but is the piece upside down in the first place?
Don't stress out when the aluminum gets scratched because it will get scratched. If it's being covered or hidden then no worries. But if it's exposed you can sand and polish out scratches but be aware of clear coating as some aluminum sheet comes with a very thin corrosion resistant coating as some alloys are more susceptible to corrosion. If it's in a high wear/scratch area you can sand a swirl pattern to hide scratches or just live with potential scratches.
And then we could talk about bending forming and welding, but that's another story.
Books on the subject.
Tune to win
Prepare to win
Engineer to win
all by Carroll Smith
I WOULD NOT try to build a GT40 without these three.
You could also add
Metal Fabricators Handbook by Ron Fournier
and
Nuts Bolts Fasteners and Plumbing also by Smith
