welcome to the forum!
ctrl-groups are just for selecting groups of ships more quickly, it doesn't actually do anything besides that. ships grouped together that way don't actually
act as a unified group. giving commands to whichever ships you have selected then can be done in two ways:
1) just right-click on a target (ally, enemy, capture point, or just any empty position on the map) to issue a context-sensitive command (which i assume you've already figured out ^^).
2) select a target with left-click and then select a command you want to give onto that target from the list in the bottom right of the screen (or via a hotkey). the game will try to automatically assign one or more of your ships to that command & target, if any of your ships are suited to carry it out.
you can then also assign specific ships yourself in the same manner as you would with a context-sensitive command, except it will use the command you've already set. the game may still keep other ships assigned automatically as well, but only if it thinks more ships are needed to carry out the command (for example, you can't carry out a Heavy Escort command with a single frigate alone. but that manually assigned frigate will be part of the escort).
keep in mind, the strategic layer of combat is meant to be secondary to the real-time parts, so you won't find the level of depth or direct control here that you would in a dedicated strategy/tactics game. there's certainly nothing wrong with playing it differently, but the game is, at its core, designed and balanced around the assumption that the player directly controls one ship in real-time combat.
if do you prefer to keep that latter part to a minimum, you'll probably want to pick up the Command & Control skill (including the Operations Center hullmod) under the Leadership aptitude, as that will mitigate the limited-command-points restriction on issuing commands.
as for your second question, afaik the only player actions that will destabilize a market are smuggling, aka trading on the black market (both selling and buying) or fulfilling procurement 'missions' for underworld contacts, and directly attacking and destroying fleets that the market depends upon (merchants, supply fleets, patrols).
contributing to stability is done through any legal trade (including on the faction's military market) and keeping its fleets safe from pirates and hostile factions, though it's generally a lot harder/slower to do intentionally.
i hope that helps. if you've got any other/further question, you can also check out our
Unofficial Discord Server, there's almost always someone there who can help you out. :]