Well, firstly, the Marauder shines most as a defensive support craft. It's essentially a Fed star cruiser with pets. Not that you can't build it to put out some okay damage, especially for PvE, but that's just not an area where it's going to excel. But she is the tankiest cruiser the KDF has to offer, and that's really where you want to put your focus when building her.
My current bridge officer layout:
Tac Team 1, APD1
EPtS1, EPtW2, Eng Team 3, EWP3
EPtS1, RSP1, Aux to SIF 2 (can switch to Cmdr slot for Extend 3 if more healing is needed)
Now, for this to work, you need at least two green Maintenance Engineer duty officers to reduce the cooldown on Eng Team as much as possible so that you don't need to run two. Two green doffs will reduce it to 16 seconds, one second above the global cooldown, which is fine to start with. However, in the long run I recommend upgrading one of those doffs to blue or higher to get it to the GCD. If you don't have enough available for this setup, that's fine. Just switch the EPtW2 to Eng Team 2. That slot is really just freed up for whatever extra bridge officer ability you want to throw in there, anyway, and if you wanted to go with EPtA or maybe bump one of those EPtS1s a rank, that's perfectly valid.
You can, if you're so inclined, switch TSS1 to Sci Team 1 if sensor debuffs are giving you trouble, and I recommend keeping an additional science officer on hand with it trained so that you can switch it in whenever applicable.
Your consoles are fine, though if you have the credits for it I recommend picking up a +35% shield rating console, and I definitely suggest getting the universal Borg console and putting it in either a tac or sci slot. You'll also want to upgrade the rest of your gear to really any of the STF reward sets, my personal preference being 3 pieces of the Borg set with the Klingon Honor Guard shields.
As for power levels, I recommend keeping a high aux setting saved for when you need to give out some bigger heals. Either 25/50/25/100, 25/75/25/75, or 50/50/25/75, depending on what you can comfortably feel you can get the most out of.
For your deployable craft, I personally really like the Marauding Force shuttles, but you can throw some repair drones or energy siphon pods in there and be credit to team as well. I also recommend running The Vault to get those scorpion fighters and deploy them as well along with your regular small craft.
Oh, and for your weapons: I recommend losing the turrets and running 6 beam arrays. You're going to get more damage that way from your broadsides and the firing arc on the torpedoes is wide enough to allow you to fishtail the ship to fire them without losing too much DPS from going outside your beams' firing arcs momentarily to do so.