How far do you mean by “longer distances”?
If you mean less than a mile, almost any method will work, as long as you have proper weight distribution to keep from straining your back.
If you are thinking high mountain lake pack-ins, then you might wanna think about a lightweight round tube, especially designed for pack in. The mini-pontoon craft are too big, bulky and weighty to make good candidates for long pack trips.
In the middle, you can use a good pack frame to lash the craft in place and trudge it to your destination. You can buy a quality lightweight pack frame, complete with scientifically attached straps and buckles…or you can get out the PVC and cement and go head on til your head hurts.
A couple of the earlier model round tubes I bought came complete with pack straps, etc. My Super Fat Cat has D rings on the underside that are strategically placed to accomodate snaps for pack straps. I don’t use them. I attach a single strap across the widest set of D rings and carry it across my forehead, like a tump line.
If you don’t want to spend a lot of time and money, you might hit a swap meet or some yard sales and look for a good buy on a used backpack. In most cases, you should be be able to adapt it to lashing down your craft. Nylon rope and/or bungee cords should get the job done.
if you need to transport your craft deflated, due to narrow trails and restricted overhead, then I might suggest this. I had thought of trying it myself. Buy or make your frame. Then attach a large chunk of light tarp at the bottom. Roll up the tube and then bring the tarp up over it and secure it at the top. You can haul a pretty good sized load that way, without being restricted by what a pack manufacturer thinks is ample space.
Let us know if you come up with a world beating idea. If you want some more input and discussion, bring it on back. I can send a pic of the “tumpline” strap system I use, or I can diagram the frame and tarp pack system if you can’t translate my ramblings.