Fordtech, I've heard that before as well, on my bike I checked the rear tire alignment using the "string method" and as far as I could tell, on my bike at least, the swing arm markings were dead on.
azpaleo, I had the same confusion when I first adjusted my chain and wasn't able to find any definitive answers at the time either. What I do is find the tightest point, push the chain up until it touches the swing arm, set my ruler (I use a digital caliper actually), pull the chain down with a moderate amount of force and check to see if the slack is within the specs.
If the chain hits the swing arm VERY easily, chances are the chain is too loose. When you get the chain within spec, it'll still touch the swing arm but depending on how far off your chain was, you'll feel that its not touching as much.
The measurement is also relative, measure top of the link pulling the chain up to the same point on the top of the link pulling the chain down (or the bottom or the middle of the link, whatever is easier).
A chain that is a bit too loose is MUCH better than a chain that is a bit too tight. As Fordtech mentioned, make sure the rear wheel is aligned properly, if this is your first time adjusting the chain and you're confident that the tire is straight already, you can use Hub's "counting the flats" trick, which is to count the number of flat parts of the adjusting nuts that you turn, or another way to think of it is, turn the adjusters equally (1/3 turn EACH side of the swing arm). This will keep your tire in the same alignment as to what you started, otherwise for the time being use the swing arm markers and if you want to verify those because you're bored to death, read up on the string method for rear wheel alignment.
After you adjust the chain and you think its good, have someone hold the bike, kick the rear tire from the back as hard as you can (this pushes the tire up against the adjusters in case it slid back) partially tighten the axle nut and re-measure. If its still in spec, fully tighten the nut, and ideally re-measure again as sometimes tightening the nut can change the chain tension.
Go for a ride, if you hear a "whirring" noise from the rear end, the chain is WAY too tight! Also, clean and oil your chain! If you're checking your tire alignment and as you spin the tire it makes a weird noise, might simply be a dry chain in need of some love.
Lastly, don't overthink this process, we're not adjusting the chain or the tire down to the micron and the more times you adjust the chain the better and more confident you'll get. Obviously you don't want the chain so tight that it'll snap, or so loose it falls off or even the tire alignment off by an inch, the closer to perfect the better but the bike isn't going to explode if the rear alignment is off by 1/32 of an inch.