[asid61]

What resources do you have? That will factor a lot in what you are doing.
To get really accurate placement of holes and edges, you should buy a height gauge on ebay. Only around $40 for a 12" tall one. Then buy a large steel plate or even better a granite surface plate. Use the two in conjunction to mark out lines and coordinates accurate to 0.001".
Invest in an angle plate, 1-2-3 blocks, or even just a good square to orient parts correctly.
We use a 36" ruler graduated in increments of .01" to mark out locations for long parts like WCD side rails. A loupe/ magnifying glass makes the small graduations easier to read.

If you can't afford the above, just get a 12" ruler graduated in increments of 0.01". Use that and a scribe to mark out coordinates for holes.

If you need holes to line up on 2x1, mmark one side and drill through with a small drill. Then drill both sides, one at a time or together, with the larger drill.

Use a punch to get hole locations accurate after you have coordinates marked out.