In the clinic where I go, they freeze the embryos separately and thaw them only as needed. In other words, if one is thawed and not viable, they go on to thaw the second one, and so forth. Last time we had three embryos frozen, they thawed all three and only one (the final one) was good enough to transfer, and it didn't take. But as mhv says, there are a lot of babies born from frozen embryos! I even know someone who got identical twins from her last frozen embryo.
They usually freeze them in groups of 2, 3 or 4, probably depending on quality.
I think the most important thing about when to do the FET, is to do it when your emotionally ready. There is alot of success with FET's too! Good Luck!! : )