Often you can take out the guard posts first, and then lure the ships away from the turrets. Otherwise, if you have an appropriate ship mix you can just move them all within range of the ships and turrets, and they will handle it appropriately for you -- they'll all fire at the best targets already, you would only need to do something different if your ship mix was poor or you were doing some clever unusual tactics (it happens, to be sure).
Non-military ships by default aren't selected with military ships, like in most recent RTS games -- you can hold Ctrl (or Shift, I forget) to override that if you want. Or, just select the scouts, then hold shift and select the military. Or vice-versa. You can also double-click a specific type of unit (like the scout) to select all of the ones that are on screen at once. You could also hold shift and then click the scout icon on the right-hand sidebar (the planetary summary) to select all of the scouts at the current planet at once.
Once you get used to it, there's tons of options for how to select various groups of units on a planet, which makes it pretty fast to do -- all of the standard controls from recent RTS games are here, plus some unique ones for this game since the scale is so much larger than other RTS titles.
Hope that helps!
