quote; I want to put them both on three ways and be able to control them independently. It sounds like having more than one 3 way on a circuit is not a good idea

IF they are NOW independent, then they will still be independent after you install the 3 way switches. You can put as many 3-way switches "on a circuit" as you want, you just can't have more that 2 controlling any given set of fixtures. In addition, it makes no difference whether the switches are at the beginning, middle, or end of the lighting "string", as long as the two switches have power and are connected together before sending the power to the lights. What you are "saying" and what you "mean" may be two different things, or you are not understanding the wiring circuitry the way you should.