My meter has a beeper option to remind me to test after meals and the default setting on that is for 2 hours after a pre-meal test and I usually go along with that. If I think I've eaten something "sinful" then I'll test an hour after starting my meal as well.
Some things, usually higher carb, starchy stuff will start being processed earlier so there'll be a rise in your glucose levels after about an hour, instead of the longer time for low carb food.
I was also confused to start with and sometimes tested 2hrs after I'd finished a long drawn out meal. But it's not an exact science just a guide, so if you'd feel happier and have got plenty of test strips then there's no rule that says you couldn't try both options and see what sort of difference it might make to your readings, for example if you've had a larger meal or are checking how you might react to a new food over time. Then when you're less befuddled/feel you've learned what sort of results to expect you can use the 2 hour guide.
Robbity