I finally got a bow mount trolling motor and it is decinitely making life easier in current. Question is, im fishing very skinny, rocky river water. I currently have the teolling motor set so it is slightly deeper than the bottom of the boat. Is there a rule of thumb for how deep you should have your motor relative to the boat to optimize performance?

No rule really.

The bow mount will work in your favor in shallow water as you can see approaching hazards.

I've had my propeller half way out of the water while navigating shallows, just be careful not to turn sharp to avoid contact of bow.

 

When you get back into deeper water, simply lower it.

22 minutes ago, Bdnoble84 said:

Is there a rule of thumb for how deep you should have your motor relative to the boat to optimize performance?

 

No, not really.  I have found that a good happy medium in terms of power and leverage will vary based on how long the shaft is.  I usually keep mine about halfway to 2/3 of the way down the shaft most of the time.  In your case, if you are running in shallow areas, raise it so that the prop can just grab water and move the boat.

Only rule is that it won’t work if it’s out of the water.  It not uncommon when retrieving a lure to surface your tm prop in shallow water.  You don’t want it banging bottom or rocks.  Always carry a spare prop and prop pin as well.  

IIRC Minn Kota recommends the prop be 12 inches into the water.  I normally keep mine around that.  When the wake boats are out sometimes I have to put it deeper.   I don't normally get super shallow with my trolling motor.