Without labels or a sketch this is a little difficult. But...
It looks like the large red wire to the right comes into the top of one of your switches. Then the jumper you mentioned, then it looks like a smaller red wiring
looping around to the left and coming back to the bottom fuse. So, I'd guess that the large red wire on the right comes from the alternator.
You can close both switches at the same time, in that case your batteries are joined together and essentially make one big bank. Or, you can close one or the other, and that battery is then used to supply the house loads, and is the one getting charged.
Very common arrangement, especially in older boats. You start the engine with only the house switch closed (assuming the starting battery is connected to the engine controls regardless of the switch position), let the alternator come up to speed, then close the starting battery switch. Just before you shut down you open the starting battery switch again.
As mentioned above, an ACR can take the place of the jumper and automate the joining of the two banks while charging, and the disconnection of same when charging stops. Personally I use switches myself, but you have to be diligent of opening the starting battery switch whenever you shut down the charging system.