I don't use cell trays. I do use 4 inch pots in flats though. I still have problems with seeds straying over into other pots and getting them mislabeled. To avoid getting seeds of the same kind of plant like tomatoes and cucumbers mixed up, I try to avoid planting different varieties of the same plant next to each other. I still get strays but at least a tomato does not look like a cucumber.
I will start different varieties in different trays. My pots are big enough to hold labels, but sometimes I have to lay the labels under the pots especially when I have to use a cover to keep the birds from eating the seeds.
If you are planting something else besides tomatoes you could separate them that way or Apple's idea of a map is good, then if I have multiple trays I only have to number them to tell them apart.
The only other thing I have tried is to plant different varieties at different times. That way they are not the same size so they are easier to tell apart.
Since tomatoes are easy to transplant, I start them in community pots with one dated label, they take up less space that way. I will transplant them to 4 inch pots later and they will then have their own label. I have fewer empty cells taking up space.