Hi Shanon!
1. Can't help you, I know zilch about bottom drains, except from what I've read here.
2. In ground ponds do tend to look more 'natural', but having them above or partially above ground makes for a nice place to sit and enjoy and some ease of maintenance. Rocks, pavers, etc can make a nice retaining wall. You can add a few rocks to your existing gardens to sort of continue the flow.
3. My pond only gets about 3-4 hours of full sun. Many pond plants prefer more sun, but if you do a little research you can find many that like shade, and there are lots of shade garden plants that will grow IN the pond (hosta, impatiens).
4. Carpet, sand, old newspaper...the underlayer is meant to protect the liner from roots, rocks, etc. Doesn't matter what it is, just thick and cushiony. Sand is better if you're putting in a preform - gives you even support and lets you get it level.

Just my 2 cents, good luck! S

Hi - I'd like to make a suggestion. You don't need a 'bottom filter' but you might want to install a bottom drain. Putting it in now is way cheaper than trying to do it later, and a bottom drain can make it much easier to drain the pond for cleaning, or if you need to repair a leak.
As far as above-ground; you can use the dirt from excavating part of your pond to raise the edges. We made a pond using cinder-blocks as retaining walls, and covered the cinder-blocks with rock for a more natural look. It was attractive, provided a seating area to enjoy the pond, and limited access to some types of crawlies we preferred not to have (snakes and turtles).
As far as sun/shade - if you want water lilies, most of them need at least 5-6 hours/day of sunlight. You'd have to hunt around for water plants that prefer shade - But you can use a lot of other perimeter plants that prefer shade, such as hostas. Having a garden pond does not require that you have plants IN the pond.
As far as underlayment goes - Like Sheepco said, anything that protects your liner from rocks, roots and sharp edges will work.

Here is a link that might be useful: I Love Koi

A bottom drain, even if it is just closed off with a valve makes cleaning a pond SO much easier....just open the valve and clean! And if you DO decide to get fish later on, the bottom drain line can be connected to filtration. You won't need filtration at this point if you are adding no fish, but I am willing to bet that some day, you'll be adding a few goldies in there. A pump to keep water circulating is a great idea though...you don't want still water getting stagnant.

I see you are in zone 8....so think about some shade. Maybe situate it where it can get good morning sun but has shade for the hottest part of the day. Plants may not do quite as well, but you will be able to enjoy the pond more if you can sit next to it in the shade rather than the sun. Shade sails are a wonderful way to get the shade you need.

I like carpet for underlayment. Call a carpet store...they usually have piles of used carpet you can haul off for free. Just make sure there are no staples or carpet tacks in it. Used carpet is all I have ever used for underlayment. It works great!