My question is that i have heard that most people are mounting the transducers under their jackplate. When you get the picture on your unit wouldn't you have pretty much passed the structure already?

Yes but that is no different than any other sonar. These units id the structure and you mark it on your gps and then fish it.

If you don't use a sonar mounted in the bow you should have a little "H" bouy marker handy and when your stern mounted transducer passes over the structure, you toss it out. You can buy 'em at Wally World, Academy or any tackle shop. Come back to it and if it's a good spot, mark it on your GPS. Just don't get it in the prop.