Conflict can be a symptom of change and a fact of entrepreneurial life. But however disagreements play out, they're not something you can afford to ignore. In a small company, even modest disruptions cause serious problems and you don't have layers of management to handle the problem for you. So, when your employees are circling other like wary cats, it's up to you to make everything right.
Don't jump to conclusions. It's easy to assume one person is right and another is wrong, but since most problems can be solved in a variety of ways, the players you're refereeing may simply be offering different routes to a win. Listen to everyone involved, but play devil's advocate, too. Make it clear that you're just information-gathering, not taking sides. You may find that an honest difference of opinion has grown too hot, or that the parties blindly dislike each other. Either way, your job is to determine the best solution for the company, not to decide winners and losers.
Get them in the same room. Sometimes listening to disputes in a formal setting can turn fraught arguments into business-like discussions. Put the parties at the same conference table and bring in some colleagues who don't have skin in the game. The goal is to invite each person to lay out his or her case and defend it. Examined calmly and even-handedly, the opposing views may turn out to be closer than anyone realized. If nothing else, you're forcing everyone to hear each other out calmly.
Take your time. As a company founder, pressure can lead you to hurry through each crisis you face, especially those that deal with personnel. But you need your team members to work with each other regardless of the strategy that's taken, so make sure everyone feels you're really listening. When you make your decision, touch back on everyone's arguments and validate their strengths. It's up to you to demonstrate that your decision was well-reasoned and not quickly made because one person got to you before the other or, worse, that you trust one person more than anyone else. Everyone's ideas count, even when not everyone agrees with them.
Step away from your email. Email is the best avoidance tool ever devised, but in this situation you can't hide behind Outlook. It's too easy for messages to be misinterpreted, with something as simple as a signoff imparting an unintended meaning ("Sheesh! He didn't even say thanks!").
Figure out what's going on in-person, make it clear that you're listening and be open-minded as you hear people out. If you approach this correctly, you'll have shown your staffers how you expect them to deal with conflict. You'll still disappoint someone, but they'll understand that you made an informed decision and that should take away some of the sting.