Firstly: I'd like to note that this post ( and the world it's based in) is partly inspired by the time travel mechanics of the game Achron. If you're confused by my question go watch some videos of that, then you can be confused by them too.
With that out of the way: Let's establish some rules for time-travel.
1: There is one timeline. While parts of the timeline may be affected by effects that no longer exist, there isn't a concept of 'multiple' timelines except in an abstract sense.
2: Any changes to the timeline propagate forwards at the same speed as time. If If I jumped back in time and didn't affect myself at all, there would be a ten year 'epoch' at the front of the timeline in which only one of me existed, but the rest of the timeline would have the history in which I arrived. If I were to jump back ten years and kill myself, it would take ten years before that change reached the point where I jumped.
3: As a consequence of 1 and 2: Paradoxes do not resolve. Instead they form multiple state 'flip flops' in the timeline. Using the example above: I jump back ten years and kill myself. It then takes ten years for me to reach the point where I otherwise would have jumped from. My lack of jumping changes the timeline of ten years ago back to it's original state, which then takes ten years to repeat the process, leading to a paradox with a period of 20 years. These paradoxes never resolve, but will continue to bounce between states forever, sending 'waves' of alternate histories (named 'epochs') down the timeline.
4: Messages can be sent between times. This is equivalent to a jump. If I send a message back to myself saying 'duck', the change it causes will follow the same rules as above. If the changed me also sends the message saying 'duck' this results in a permanent alteration to the timeline. If the changed me does not send the message, a paradox results.
5: It is not possible to detect when a message or traveller has come from (unless the message or traveller tells you), and similarly it is not possible to detect (without prior knowledge) where a message/traveller is going to.
Ok. That's the rules out of the way. Now onto the scenario:
A war has been raging, using time as a battlefield. Nobody knows how long the war has been going, because it's been lost in a haze of paradoxes and time loops. The war is formed into roughly two sides, and at some point these sides have managed to organise themselves with centralised command structures. It can be assumed that any soldier on either side will immediately and implicitly trust any messages they get via the time-communication devices, and that neither side can interfere with the other's time- travel technology directly.
My question is this: Given that the paradox mechanics can result in constantly changing histories, and Epoch boundaries move forward through time constantly, how can either side establish a permanent command structure that won't eventually end up sending orders over itself? So far all I've come up with is jumping back as far as possible and setting up a (very well hidden) command post.
Please note: This isn't actually of vital importance to any plot elements at the moment, but it's been bugging me that I can't think of a decent way to do it, and if I were to expand this world past the current narrative I've got going I'll have to address it.
Addendum: You can assume that this universe is deterministic and ignore the vast majority of quantum level effects. Unless a traveller/message has an actual interaction with a system it can be considered to evolve in exactly the same way. As an example: If a traveller jumps to where a lightning bolt will hit it will route through them. If they jump twenty miles away the bolt will take exactly the same path as it would of without the jump occurring.