Depends on the motor. I know on 5s-fe's and a 3vz-fe's the signle dots are factory assembly markings, while the double dots are the timing markings.
Be sure you get the distributor timing correct, and that you're not doing something retarded like timing the entire thing TOD of the wrong piston. (Yeah I did that once.

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AFA timing the distributor. Every Toyota engine I know of, if you're @ TOD of the compression stroke on the #1 piston, the distributor's rotor should be pointing at the #1 spark plug position.
One important thing to remember, if your car takes the crank signal from a camshaft sensor, then you need to be top dead center of the compression stroke. If it get's the singla from the distributor like a 3vz-fe, then it obviously doesn't matter either way.
be sure you're timing with the correct ECU pins jumpered to get into diagnostic mode too.