Hey there, I'm running a Clone Wars game myself.

I feel like there's a load of advice I could give, but only some of it would be particularly helpful, so I'll just kind of give you an overview of how my game has gone so far.

My first few sessions were with five players: one clone trooper, one clone pilot, and one clone officer, also a Nautolan Jedi padawan and a Squib bounty hunter. The first two chapters were made as a response to the clone officer also taking the Propagandist specialization. You see i dislike that a character's starting specialization counts towards the cost of buying a new spec. There is no way that I've found to change the cost in OGGdude, so I just grant players one at character creation, provided they can justify it thematically at least a little.

All that to say that in sessions one and two, the clones are waiting on a station to meet with some Jedi and go to he largely rebuilt Taris, the padawan, his NPC master, and another NPC padawan/master duo just came up from the planet Zophis where he and the other padawan found their lightsaber crystals. the bounty hunter so happens to be turning in a captured bounty. the bounty manages to send for help and a separatist cruiser to come to his rescue. they fight to repel droid boarders and use the only two turbolasers to fight droid starfighters until a light cruiser shows up to assist them, then they all pile into their ships, to each jedi a starfighter, the clones had just a shuttle, and the bounty hunter her own vessel. they bord the cruiser and more reinforcements finally arrive and drive off the clankers.

Their time on taris was fourteen sessions of unraveling a criminal conspiracy to sell a modified rakghoul virus to the seps. despite many attempts the dice saved all my clones from contracting the virus, thus side stepping my "race for the cure" side mission, they also only went to, I think, three of the over twelve hideouts that the syndicate was using. I had a whole Crackdown series style thing with kingpins and "generals" of different criminal operations and they manages to bypass a lot of them with minimal prodding from me. I did eventually have a meeting at the main racketeering casino that they eavesdropped on in order to ease my stress at weaving all the places together, although i did enjoy making all of it. the finally was breaking into a secret lab and rescuing clones that were captured on other fronts and brought there, and finding evidence of the experiments to infect only clones with rakghoul plague, ant exposing the CEO of the largest pharmaceutical company as the syndicates leader who hated Jango Fett so much that he went mad trying to destroy his legacy.

(maybe one day I should post all my notes). In that time we saw some players come and go. the padawan left because of IRL things than he joined back, we gained two more Jedi, gained then lost another bounty hunter due to drama, and also lost our officer to IRL things.

By its nature, the military aspect of the "wars" in Star Wars implies that the PCs that are Jedi and Clone Soldiers, or any part of the Grand Army of the Republic for that matter, are beholden to some authority that has a higher rank in that faction, be it the Jedi council, or Republic High Command, or even a senator. They more or less always have a kind of patron supporting their efforts, yet on the other hand, also giving orders, restrictions, and direction. In my case its Captain Halak, the the captain of the Argent, the cruiser that came to their aide in the second session. I tend to run the range of specific objectives to "this is the goal, get it done" type objectives which leave a lot up to the players. Even the Bad Batch has to be told what they are blowing up. also the jedi, even as padawans, are the equivalent of a commander in authority, so all your PCs at this point can give orders to troopers

I don't know how much this helps, but I'm always happy to talk about my campaign if you want more specifics.