I understand your situation very well. We have 6 kids ages 11, 11, 9, 6, 3, and 1. My husband travels 90% of the time. I'll let you know what we've done (although we're not perfect!)
Has your husband had a chat with them to let them know his (and your) expectations while he's gone? They may need a reminder from HIM that you're still the boss when he's gone and that if it's a problem, he'll deal with it when he gets home. Some Bible study about the servant leader might also be very appropriate for their age.
Do each of the boys have specific daily household activities (ie. chores) that give them specific responsibilities toward "being the man" while Dad's gone? A great website to check out is www.activeallowance.com . They have charts you can print (free) and include both duties and behaviors, like "Be kind, no fighting, bossing". They seem to help our kids stay focused on our expectations.
Another thing I've noticed is that sometimes they need reassurance that everything's OK with Mom and Dad. Not necessarily beig told, but if you talk with your husband on speaker phone (unless something needs to be private) they have a chance to pick up that everything's fine just by hearing your conversation and tones of voice. Another great option is video phone via internet. We haven't gotten that one worked out yet, but really want to!
One last suggestion...if your husband is gone for long periods of time, look into getting an older male buddy from church for them to hang out with. A responsible older teen or another man just to throw a football or grab a burger might fill their need for male bonding. Boys learn how to be a good male leader from watching other men, and they're getting to an age where being more "manly" becomes more and more important. At the same time, they still need to recognize your authority over them.
Good luck!