More than one Mechanic question?

I think you need to give us more information on the stages of play and the different mechanics if you want other designers to comment on your particular situation.

Your statement is sorta "The sky is blue."... And what, you want to know if there will be clouds, when the sun will set, if an airplane will pass by, etc.

If you provide us with more information we may correctly be able to respond to your concerns.

That's still not quite enough to go on to provide useful help, but here's an idea off the top of my head:

This sounds pretty similar to combat in Warhammer 40k. Each player's turn is broken up into 3 phases: Movement, Shooting, and Assault (i.e. close combat). Assuming you don't actually move any of your ships around, you can ditch it and stick with an equivalent Shooting and Assault phase.

In the Shooting phase, one of your units targets an enemy unit within range and line-of-sight, and you roll dice for each shot to see if you hit. From the shots that hit, you roll again to see if they are strong enough to wound, and then your opponent rolls for each wound to see if they can save against it.

The Assault phase works similarly. For each model close enough to engage in combat, you roll a die for each of their melee attacks to hit, then to wound, and your opponent rolls to save against them.

The basic mechanics of ballistic and melee combat work out pretty much the same, with a few minor differences in which stats to compare or which models can make attacks.

It sounds like your game is similar, with a ship-to-station shooting phase and an assaulter-to-defender melee phase.

EDIT: I just realized that I didn't really answer your question. I think the point I was trying to make was that you can probably find a way to use one mechanics for both phases. Having separate mechanics for each phase isn't strictly bad, but it could potentially be confusing or feel disjoint for players. Making them similar would help the player stay in the game more, and it's always less rules for them to have to learn.