In the future plant them in individual small containers, party cups or seed starters of some sort. You want to transplant smaller containers into big ones so you don't have to mess with the roots and injure the plant during transplant.
I would transplant asap, I would use a tube/pipe with thin walls to take a "core sample." You want to get those out of there before the roots spread and force you to injure the seedlings during transplant.
By core sample I mean, cut a cylinder of dirt that includes the seedling's tap root.