Fantastic that you've gotten into kayaking and want to do some trips. A few things to consider:
Getting some help may be, well, helpful - getting out of a kayak on a steep sandy beach with waves and trying to get into a wheelchair right there probably wont work, so some assistance may make things go smoother and safer.
A wheel chair could possible go on the deck, but the salt water may damage it, and it would make the kayak less stable.
Some remote campsites have sand, logs, rough dirt paths with roots and rocks to scramble over.
Since you're new, my suggestion is to have someone drive to the campsite with your wheelchair - a campsite with a road to it will likely be a bit more developed. And use the experience to sort out your systems- what you need to camp, what you can do without, potential challenges and solutions. Once you've figured that out, getting to more isolated campsites will be easier.
There are adaptive kayaking groups, clubs and programs out there. I'm sure they would have more specific useful advice.
Cartop Kayak Carriers
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