If I hooked two batteries together...can I run a 12 volt trolling motor and my electronics...thanks

The trolling motor will interfere with your depth finder. Keep them on separate batteries.

OK I will keep them separate... But will two batteries connected together burn up a 12 volt trolling motor???

Depends if you hook them up in series or parallel

I had my two batteries hooked in parallel (+ to +, - to -) and ran everything off of them.  Motor, electronics (Eagle, Helix and a 999), TM.  Had no interference issues at all.  I know it is not the accepted method but it worked for me.  12V to everything and double the run time.  Never ran out of batteries even with the TM on 4 or 5 all day.

I have an older (2002) 12V MG 5-spd foot control TM so that probably helped.  Now I'm upgrading to a 24V system with a digital MK so everything will be separate.  The TM on one circuit and the electronics/motor on a second. 

My first assumption is you are speaking of identical batteries that you are wanting to connect together.  If you are not talking about identical batteries, it's not recommend you connect them together.  Connecting dissimilar batteries in parallel is not as damaging to the batteries as connecting them in series but it's still not a recommended practice.

If your TM in one that has the set number of speeds, like 1,2,3,4,5.  Most  likely your TM will not cause interference on the sonar.  It's normally the Variable Speed TMs that cause a problem.  The filtration in most sonars will filter out TM interference.  

Hook them in parallel, Positive of battery A to positive of battery B, and negative of battery A to negative of battery B, with Positive TM cable to Positive Battery and Negative TM to negative battery.  Try it and see if it going to causes a problem on the sonar.  It's not going to hurt the sonar, if it's going to interfere, usually it just make a black area or blanks the screen for a couple of seconds when you press the run switch.  If nothing abnormal happens, run it.  However, if you run your TM batteries down, it will probably make the sonar shut off when you run the TM because of the low voltage.

If you can run the batteries in parallel, it will give you a long run time than swapping them out because it make the batteries much more efficient. 

The batteries would put out 24 volt if you cross the positive with negative.

So, just connect the positive to the other positive and then negatives to each other and you will still have 12 volts.