Assuming you have access to the GECK, you could very easily make the Enclave soldiers you command with the Enclave Commander mod and the regular in-game Enclave soldiers allied with each other and yourself (just set the player faction to be allied with the Enclave faction). Then you could get a mod like "sharing and caring companions" to actually be able to command the in-game Enclave soldiers.
I mean ultimately the RP situation is up to you, what I explained above is what
I do. Along with a variety of other mods I've got it to where I RP a member of an Enclave which is under Eden and in which Autumn and Eden aren't in conflict ideologically.
Also, if you have the GECK, try setting "Liberty Prime" to be able to be destroyed (remove its "invincible tag") and then join the Enclave soldiers on their side of the battle. Makes for a hell of a fight (might want to get a mod to improve the Enclave's armor though).