You can force the game to split your sats into two Groups, but only (really) for planetary defence:
Keep half your satellites in orbit and the rest in cargo storage. When combat begins, there will be your orbitting satellites in one group, and then the planet can (should, in strategic) launch the remaining satellites into a second group. This has obvious limitations (ie cargo space) but in Proportions mod for example, where breathable worlds and especially homeworlds have huge amounts of cargo space, it ought to be viable.
For full planetary coverage throw a couple of defence stations up as well. I guess if you built stations with cargo storage & sat launchers you could have even more sat Groups.
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A cool idea: The "Satellite Snail"
Build a transport (biggest you have) with a low movement rate (maybe 2 combat movement) and a single weapon. Fill up the rest of the ship with sat launchers, cargo bays and sats. It should be fairly cheap to build and maintain. Give it primary orders of "point blank" & "don't get hurt" as secondary. Leave a few of these in orbit of your planet and when combat begins they will begin crawling slowly toward the enemy, leaving a trail of armed satellites in a line between the attackers and the planet.
The enemy ships will waste time and firepower shooting at the sats on their way to the planet, all the while messing up their formation and taking fire from your satellites & other defences.
The "snail" ships themselves will soak up some weapons fire when they reach the enemy and might get destroyed. However if you pick a weapon with a high damage resistance it probably will be the first component to be destroyed. Once a snail is unarmed the enemy ships will probably lose interest and your ship can crawl towards the safety of a corner.
Has anyone every tried this out? It's probably cheaper just to use fighters... Am I the first person to think of this strategy?