Yes, you have options...
Don here from Confluence Kayaks. I've done some kayak outfitting for a person with an amputated lower leg. You've got a bunch of different options. Some of the things that you need to think about are: where is the power coming from? Is it shin, knee, thigh, or hip? Then you want to think about supporting the leg properly and dealing with any comfort issues. Here's one that you might not thought of... weight. You may need to compensate for weight differences between one side of the kayak and the other. A little counter balance under the seat works great.