Once the war is over, it'd look like Roy & Hughes follow different paths for their lives. Hughes gets married to Gracia and stays in Central City, still working for the military (investigation procedures, it would seem). Their daughter, Elysia, is born approximately 3 years after the war ends, in 1912. The Hughes family is an extremely happy one, loved and admired by many. Hughes himself doesn't hesitate to brag about it in front of anyone.

Meanwhile, Roy gets assigned to East City, where he begins his quick and calculated ascension through ranks. He manages to reach the colonel status in barely 2 years, via what can be described as a perfect combination of hard-work, social skills and estrategy. It's also at this time when Roy starts to gather up the people who would be his closest workers: Riza Hawkeye (she asks to join him after the war), Jean Havoc, Heymans Breda, Kain Fuery and Vato Falman.

     

Of course, given that Hughes was quite the detonator to Roy's decision to ascend to the top, it didn't matter whether they lived in the same city or not. It's obvious that Hughes would go to any extent to keep helping Roy to achieve his goal, no matter how apart they were physically. His support was unconditional, and never failed to make a phonecall to inform of any piece of news which could be valuable to his friend.

Hughes: You probably find it hard to believe, but this means there's a guy that dangerous lurking around this city. I'm telling you this for your own good. Just increase the number of escorts around you. I'm asking you to do this as your friend. If he's going after well-known people, that would just leave Tucker and you, right? Since Tucker was done in like that, as long as you're at least careful...
Roy: This isn't good...
Hughes: Hey!?
Roy: Confirm if the Elric brothers are still at the inn. Immediately!

The biggest problem you encounter when trying to protect Roy Mustang, is that the last person he worries for is himself. Hawkeye and Hughes know this by heart, and little by little other people start to notice it too. Still, he's not a reckless man (at least not normally), he's just got priorities... and self-protection comes very low in his list the moment others are in danger.

One of the main differences between Roy and Hughes is also the part of them they choose to show to people. Roy projects serious politeness at first sight, he's a reserved man who takes his time to open up to others. Despite this, Roy's not throwing signals of his tortured inner self at your face, he's reserved for all of him. There's also the fact that he's trying of mislead people so they don't notice what he's trying to do. The real Roy appears when he's in front of the ones he trusts, though.

Hughes, on the other hand, chose to project a happy-go-lucky image to his surroundings. He usually acts open-up and warm and is welcoming to everyone. He sure behaves that way naturally (we can see he was like that even before Ishval), but it was also his decision (and he said so himself) to eat up all his darkest experiences and offer his family and friends a smile, it was his way to achieve happiness.

Either way, and despite their differences and ways to live their lives, both of them knew the other, understood their reasons and accepted their friendship just as it was. Mutual understanding.