Thanks for your question and your kind words about my work with llamas and alpacas. When it comes to males and behavior it may be interesting to try and figure out where the behavior comes from or whether dominance has anything to do with it, however the bottom line is that changing the environment is the only real way to make things work. You are already on the right track here when you mention that the water is available to both animals but to make it possible for these two to share space you will have to make some changes that provide all the "services" to both animals. This may mean rearranging things so that both animals have equal access to shade, water, and food.
One thing to consider if you haven't already, is whether or not there is a part of the pasture that affords better access for viewing females. If your males have not previously been fighting and have recently started, it may be that girls are suddenly much more important to one or both of them and that there is a part of the pasture that provides better access to viewing females. If this can be changed you might see an improvement in the behavior. Bottom line unless you are willing to move out to the pasture to keep the peace you have three alternatives:
1 To separate the males (not ideal from many points of view)
2. To change the antecedent arrangement (the environmental situation that provokes the behavior.) This means to move things around as described above so that the animals do not have a reason to fight.
3. Gelding one or both of the animals-- although with this choice you will probably still have to do some rearranging until the hormones stop flowing.