It depends on whether you want to go the ornamental pond route or you want to be completely natural. If you want it ornamental, then you would treat it like any other garden pond. Lilies and other plants would be potted up in pots and repotted as needed. Cleaning a pond such as that is pretty easy compared to the natural method. A natural pond would mean you would cover the liner with a foot or more of clay dirt (or perhaps no liner at all) or fine gravel. The plants would grow wild. Cleaning would be very hard.
For a pond to support plants, the plants need a substrate. You can use clay soil, aquatic pond soil (sold), plain clay cat litter, or pea gravel. The first choice would include some nutrients in the soil and would work much better for plants like lilies. The plants could be fertilized with aquatic plant fertilizer or naturally with wastes from fish, tadpoles, and/or other animals.
Maintenance for a plant-only pond would be similar to a regular pond but perhaps the filters wouldn't have to be as elaborate. I still suggest some water movement and filtration to prevent stagnation and deter mosquitoes. Plants require fertilizing and repotting on a regular schedule.
See my plant care page at
http://www.fishpondinfo.com/plant.htm for more information.