It probably will not hurt anything, but is not the right way.
The recommended way is in a two motor installation, each motor should have its own battery.
Here is a potential solution to your dilemma....
If you do not want to add a second battery, you could install a battery switch but install it a little differently than a normal battery switch wiring.
1. Connect the battery positive lead to the common terminal on the switch.
2. Connect the positive lead of the big motor to terminal #1. Connect the positive lead of the small motor to terminal #2.
3. Connect the negatives of both engines to the negative terminal on the battery.
When you want to run the big motor, the switch should be on #1. It will charge the battery.l When you want to run the small motor, the switch should be on #2. Then the small motor will charge the battery.
If you want to run both motors at the same time, you will need to have the battery switch on #1 to start the big motor....leave it there. The big motor will then charge the battery. If you turn off the big motor, turn the switch to #2.
Never switch it to "all".....you will then have the same connection you have now.
Hope that was not too confusing or too much of a contradiction to what you have already been told.
Mike