There are a number of ways to do this and only a few would be considered best practices..

We really need the brand & model of the thruster and the battery size & type in the bow in order to be more helpful..

On a 35' boat generally the easiest and best method is to run bow thruster wires from the house bank to power the thruster. You then feed the alt directly to the house bank charging the start battery via a combiner or battery to battery charger.

 

Yacht Thruster S180 by eXturn. 12V and it says the nominal current is 187 A

Bow thruster battery is a Grp 24, 800 CCA marine start battery. The install is complete with the battery mounted in the bow immediately above the bow thruster. Standard battery cables with Pos run being 36 inches thru 100A OEM inline fuse and Neg run being 24 inches.

The install is complete. The boat itself has a Grp 27 Marine start battery for the engine and two 6 V golf cart batteries in series for the house bank. The engine start and house banks are charged by either the alternator or the A/C battery charger. I have also run 6 AWG Pos & Neg cable (30' ea) from the bow to the engine compartment for possible use in finishing the project.

I am looking for the best way to safely charge the battery in the bow.

 

One alternative would be use an ACR/battery combiner to automatically charge the battery. An advantage to this approach would be you could run much lighter wires to the bow versus what you would need to run if you were to power the thruster from the house bank. You could do it with a battery switch, but an ACR will take care of it automatically.