If you get a chance to do some research you'll realize the answer to your question is a somewhat obvious one. If you have a Minn-Kota with ipilot, the only way to go is Humminbird. I am not an expert by any means, but I've been looking into this in depth recently. My father-in-law purchased a Lund from Crowley and they were trying to sell him a Lowerance for his new Ulterra. After some research we realized that was terrible advice. (Not digging on Crowley, I just don't think the salesman had much knowledge of this pretty complicated subject).
Lowerance, while compatible with the Minn-Kota transducer, is not compatible with the ipilot function. By installing a Lowerance you are missing out on an opportunity to add tons of fishing advantages offered by linking your fish finder unit to your motor. Linking the Minn-Kota to your sonar/gps allows you to control the motor from your unit. You can tell it specifically where to spot lock, to follow a contour line, or navigate to a destination simply by selecting a sonar blip (fish/structure) or location on your screen. You can also record many more spot lock locations and tracks.
I am in the same market as you and I was originally looking at the Helix 7. It won the ICast best/most affordable fish finder award last year so I thought it was an obvious place to start. It will do everything I stated above and then some. However, I'll be purchasing the Helix 9 for one reason, it includes the AutoChart live function internally. It allows you to map a lake while you are fishing it, and even better yet, the maps you create function with your Minn-Kota. Meaning you can map a hump or a shoreline on a lake with poor contour maps and use that map to follow the contour which works great for trolling/jigging/casting.
As for transducers regardless of what unit you chose you will be doing a great injustice to it by using the Minn-Kota transducer. The Minn-Kota transducer will only function as a 2d sonar. Which is your traditional "arch" sonar screen. Whereas the transducer that will come with the unit (depending on which one you purchase) will also provide down imaging and/or side imaging. Giving you a handful of more tools to help you catch fish.
Something extremely cool about linking a side imaging unit with your Minn-Kota allows you to mark schools of fish up to nearly 100 yards on either side of the boat. You can then move your "cursor" to a school of fish and tell your motor to "Go to" that spot. Your motor will proceed to take you to the exact location you marked the fish and spot lock. Its almost like cheating...
My father-in-law installed the Helix 9 and we've been using/playing with it for about 2 months. The functionality has been amazing and its very user friendly. Watching the AutoChart function in action made me realize its versatility. Most of the contour maps for Colorado lakes are pretty poor, specifically for all of the reservoirs. With this function you can map a spot in 5-10 minutes and have an extremely accurate contour map that no one else has. You can imagine how that will give you a strong advantage over other anglers or even just help you catch more fish.
Sometimes the new units have so many functions it can be a bit overwhelming for people that aren't tech savvy. Especially for people that are switching from Lowerance to Humminbird since they have different user interfaces. My father-in-law was skeptic for this same reason, he had an old Lowrance and jumped up the the Helix 9. However, he got it very quickly after spending an hour or two with it in the driveway. You can get a Helix 9 with down and side imaging for around $900 on Amazon.
There are tons of videos on youtube. If you do a couple of quick searches that will be very informational. I suggest taking a look.