When drilling, everyone has their own opinions. Templates, measuring, unibits, drill presses... they all tend to cross paths but ultimately everything is up to you to find what works best. IMHO, there's two aspects to drilling: The setting up of the jig or it's environment, and the placement of the holes. Get those things set up properly and you're sure to have good results.

Firstly the setup:
-What I personally have arrived at is that I still like my good old hand drill. I have a drill press, but I prefer to use my cordless because a) I can change bits out more quickly and b) I like having the speed control at my fingertips.
I still use a jaw-vice and advise everyone to use one. Here's my 4" vice which works for up to 1590BB sized enclosures:
http://www.harborfreight.com/cpi/ctaf/displayitem.taf?Itemnumber=30999Then there's the drillbits: I don't like to skimp on the standard ones. Carbide, Cobalt or some kind of Oxide is good. (Steel or Metal compatible.)
Unibits (or step-bits) are too expensive from HD or Lowes, so in that case I go for the ones @ Harbor Freight. I've had this one since 2000, so do you really need a $40 one?
http://www.harborfreight.com/cpi/ctaf/displayitem.taf?Itemnumber=44460 Step bits are great, but are not a cure-all! For one thing, they can "walk" towards one side of the hole, which can really misalign your hole. (Also, sometimes the hole size you need is all the way at the top, and you may not be able to drill that deeply into an enclosure for myriad reasons. )
For bigger holes (Say 3/8" or larger) drill a 1/8" pilot hole first.
So decide on how you want to drill it. Now move onto the marking your holes...
-Got any painters tape? That makes measuring easy. I like the 1" blue stuff. It's faithfully
exactly 1" wide. Why is that so great? I'll try to include some pics, but visualize this with me: Take your enclosure, and lay a piece of tape across it. Eyeball it, it's OK. Make it as perfect as you can get it. Let's say approx 3/4" from the top. Now lay one right up the middle, perpendicular to it. Make it look like a perfect cross, basically. Again, eyeball it as perfectly as you can. This is great because the cross is so forgiving! (No pun intended.) If you look at it at arms length and it's not straight, you can easily straighten it up and there's no permanent marks to confuse you later.
NOW you can get your ruler out. Draw lines up the middle of both pieces of tape at exactly 1/2". Easy! Now you have dead center lines! Makes all your knob placement from there super easy! You now have a center to measure from, and linear lines to measure from! (I'll post pics, but this is super easy to do. if you can make a perfect looking cross, from there it's easy)
Now some measuring comes in, but it's all up to you. Mark where your potentiometer, switch, and LED holes go with a
light tap of a punch if one's handy. (This keeps the drillbits from walking.

)
Move onto the holes on the sides for the jacks. With the bottom lid off, wrap a piece of blue tape again around the backside, coming up over the sidewalls. Again, measure 1/2 the width of the tape, which is exactly 1/2", and you've now got centered jack positions! I've found 3/8" or 7/16" up from the bottom of the sidewall is a good magic number to shoot for.
Now all you have left is to decide where the DC jack goes. That's up to you, but again I use 7/16" from the bottom of the sidewall.
Pots, LED, Switch, Jacks & DC Jack. That's mostly it! For a one off pedal, this is a quick and easy way to go with great results!
I can list what size holes I use for components, but not everyone uses the same stuff so it might get confusing. Like I said, pics are on the way!