Artemis is generally considered longer range, mostly because it turns slow. It's still effective at close range for damage and such, just harder to track enemies.
A lot of mobulas go with a hybrid of close and long range, whatever your main range is (close or long) you should have those guns on the lower deck, allowing the engineers to be closer to hull and balloon. Some players just put the close range guns down there, so the engineers can be closer to those components while the enemy is close, and the ship is more likely to take damage. Suppose it really depends on the enemy (a long range enemy will damage your ship just as easily at range, and your crew is going to have to keep running up and down the ladder to try and deal damage and keep the ship repaired).
Personally I like the hades a lot more than the merc, so I'll generally go with hades top, then double artemis or artemis-flack on the bottom (Then the wings can have a flare or carronade-flamer). A nice brawling mobula is having gats on the lower deck, and a mortar up top. Flak is ok, but has that arming time that makes it difficult to use, artemis on the wings isn't bad.
My favorite mobulas are similar to what Hamster posted, with either a double merc or preferably a double hades on the left or right side. No other ship can get a double merc in arc with an artemis, and it can be pretty devastating. I still prefer hades over mercs, but you need to have the gunners for it. Dealing with close range is a bit harder of course. I'll usually have an engineer up top and the gunner and another engineer on the wing. When things get intense, the top engineer will hustle over to the non-manned side, and the gunner can get up top. It's not ideal of course.