Serum DEX needs to open a "trading account" the FIRST TIME when you trade a new pair.
All future transactions of that pair will only cost just gas (miniscule amount in SOL).
I know this sucks but its how it is designed.
You need to 'Claim' your items from Inventory ⬇️
Next:
Go to your 'Faction Fleet'
For each class of Ship, click 'Manage Fleet'
Then hit ->'Repair Fleet'.
Approve txn from wallet.
Click 'Resupply All' and approve txn.
Repeat the same for all varieties of ships in your fleet.
Yes, I know what you are thinking. For now, it needs a lot more clicks but I'm sure as the team receives more feedback and the Fleet Management UX is likely to improve.
Plz let me know if this helped, you can always reach out to Star Atlas community in their Discord for doubts.