If you are going to use a sidevu or sidescan type sonar, the thru hull will hang down and should be on centerline to give clear sonar path on both sides. Thats a problem with single engine boats because it may disturb water flow to engine. There you best bet is a transom mount starboard side between motor and trim tab.
If you don't need side scan but want a CHIRP transducer there are flush thru hulls like a B175. There you just look in your bilge for a place it will fit.