I have 46 gal tank with a Penguin BIO-Wheel 350 filter, and a Rena Filstar xP1 canister filter. I have also been using a under gravel filter system.
I have read different things on many web sites. One said to use little or no gravel, and others have said use at least 3 inches deep.

Please help me out here, I just did a complete tear down of my tank and really dont want to cycle it twice.

You really don't need the undergravel filter with those other filters. I don't really like undergravel filters (UGF's) as they make the gravel more dirty and end up holding things like waste and fish fry under the plates. They also require complete tear downs to clean under them. If you don't have any huge fish or digging fish that will move the gravel around, I think 2" of gravel over the UGF is enough. Three inches is probably okay as well. I would be sure to do weekly or bi-weekly gravel vacuumings of the gravel to remove whatever is sucked down into it. To some extent, the more gravel that you have, the more good bacteria can grow in the gravel of the UGF. But, your others filters also have biological components, and if you have too much gravel, then it starts to harbor wastes and pockets of gases (which also occur in gravel without a UGF). It's also harder to clean and takes up room. If you have huge fish that root around such as some cichlids, then more depth makes more sense.

So if I take out the UGF how deep should I keep the gravel? Or is there somthing better than gravel I could use?

Just use regular aquarium gravel. I prefer natural colored with stones about 7-9 cm in size but that's just personal preference so it's up to you! As for depth, without a UGF, 1 to 2 inches of gravel is fine unless you either have big rooting fish, or you wish to have live plants. With live plants, you need room to plant so the 2" depth is better and sometimes 3" with larger plants.

Some people use sand but it's messier, hard to clean, and can harbor pockets of anaerobic gases. More course sand is good for certain fish that like to pick up and spit out small stones or for fish that need to bury into the substrate such as freshwater stingrays. But, for us average freshwater fish keepers, regular aquarium gravel is usually the way to go. Also, some people prefer no substrate as it makes things easier to clean. I don't think it's very natural though. For the natural look, you could use dirt but you'd have one huge mess every time water moved over it from mechanics or the fish! In my ponds (where I plant pond plants in clay dirt topped with pea gravel), it also starts to stink after a while!

Thanks for the info Robyn. I think I'll take out the UGF and go with just the gravel. I have been thinking of adding maybe 2 small plants to the tank any way.

Thanks for this web site you are a great help, and I'm glad someone like you takes the time each day to answer all the questions every one has. :)