If you have the time to wade through it, there are a lot of good clipper tips here:
http://modified.in/footbag/viewtopic.php?f=15&t=6010
Clipper is a really tough trick to learn to begin with, so don't be discouraged. Once you start getting it a few times, it will really rapidly improve. I would say there are three aspects to it;
1. Flat surface. You can work on this without a bag. People have different degrees of ankle flexibility, and most people find that this also improves with time. If you're not very flexible and having trouble getting a flat surface try bending the support knee more and holding the stalling foot further off the ground. You don't need a perfectly flat surface, but the flatter the better. Practising inside stalls will also really help, and actually clipper requires less flexibility than inside stall, so it sounds like you're on the right track.
2. Co-ordination. It's very common for people starting to not be able to get their foot in the right spot, and you end up completely missing it, or having it land in the wrong spot on your foot. I think you should aim for the middle of the inside right down on the edge of the sole. A large part of getting it right is just practice. If you can do things like hand set>clipper>hand catch and keep practising that, it's a good place to start. The other thing that helps is trying to get your head directly over the top of the bag so that you can literally see that your foot is under it and in the right place. This helps a lot with your balance too, because it means your weight is straight above the support leg.
3. Timing. This is really the "secret" to clippers. Like with all stalls you have to make sure you're cushioning the bag as it hits your foot. This takes a lot of practice to learn, but will eventually become natural and automatic. A big key to this is doing a little hop so that you're landing and cushioning as you stall the bag (the so called "magic hop"). This helps make sure you're in position too. Cushioning and setting should be a combination of moving the stalling leg up and down, but also bending and straightening the support leg. As you land from the magic hop you should bend the support leg down a little, and then straighten it as you set.
Remember that it is hard, and will take practice to get consistent. Try to keep both sides equal, and if one is worse than the other, spend more time practising that side. Good luck
