I think you will be fine if either the single or double dots are lined up since once you rotate the cams when they are in, the 2 double dots and single dot pairs will be aligned as they pass by each other, no?
You can see a few photos of my 3vz-fe hg job on photobucket. Here is a pic of my cams aligned to the single dots which is the resting position they were in at TDC for cyl #1:
The real question though is are the back and front cam pairs aligned using the same single or double dot pairs for a given cam position once the belt is back on? I can't remember that. You should be able to figure that out though given the firing order.
dave mc