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Ok I am planning on getting a congo puffer. They need sand to dig in so that's a must. However, they also like plants. What is the best way to go about getting plants to grow well in sand. Potted plants? Java ferns tied to rocks? Also, any tips on preventing sand from ruining a filter?

If I were to do sand, I'd probably use small terra cotta pots with laterite in them for plants like crypts, vals, and maybe some particularly robust stem plants, but I'd go mostly anubias and java fern tied to wood and/or rocks. If you have MTS to stir up your sand, you might get away with planting them directly in the substrate, but the pots are more of a sure thing, and you can bury them in the substrate to hide them, or coat them in aquarium silicone and roll them in sand or gravel or even stick bits of rock and wood to the pots to make them look more natural.
As for your filter, I definitely suggest putting some filter sponge over the intake to trap the sand before it gets to your impeller. This will also provide added bio-filtration.

Hoping that there must be a word for everything I mean...

II have a few sand tanks, and I have had little problems growing plants in them though I know that the sand being small can compact the roots to much. I have actually found that you can mix half and half sand with incomplete and actually it is what I plan to do on this move Adding a small sponge to your intake however is a MUST I added a small bit of it to the intake between the first and second extension tube so that it isn't getting leafs stuck on it. It will also prevent a lot of the larger detritus from getting into the filter and I see it as it is getting bad. It also holds it in place because of the second strainer, and is much less of an eyesore. Other then that, remember that your plants WILL get nipped and stem plants with get cut in half because the puffers like to look for snails sitting on plants and if they see something that they think is a snail they will nip the plant. Just my two cents.

I have a sand-bottom 12g tank. I'm using pool filter sand which is a larger grain size than some of the other sand you see. Plants like wisteria are growing fine in it. I also mixed in some eco complete in the back area of the tank for some other plants. Just have the filter intake about half way up and you shouldn't have much of a problem.

I would also spread the sand pretty thin or you might have anaerobic bacteria activity. Putting in a few fish that "run" through the sand like kuhi loaches will also help bring oxygen into the substrate.

My Scapes

The more plants you plant the smaller the possibility of the sand going anaerobic adding loaches really would help some cory would also. I am in some of my tanks using the ram horn snails which in this case the puffers would eat if you don't have enough of them. Some puffer keepers say that those snails can break the puffers beak tooth however.