I forgot you had such a small tank. Sounds like the siphon is pulling out water faster than you can get it around to clean enough of the substrate before you are too low on water? I know they make tiny "Beta Vacs", mini vacuums, etc. Maybe look into those? The other option would be to bend the hose at the top of the actual plastic tube, right where the hose starts. Kinda like kinking a garden hose. I do this to slow the flow sometimes. But if you slow the flow too much you aren't sucking much out of the gravel either. I think finding the smallest gravel vac possible is the best idea.
The amount of water it is safe to change is debatable, you'll get a variety of opinions om that. I think a lot of it depends on how well you prepare the replacement water. For example, my planted tank is a bit more complicated, but I use RO water, and make sure to match the kH (carbonate hardness) of the water in the tank. If you are using treated tap water, and doing regular (at least weekly) water changes, you shouldn't have to worry too much about that. You should be able to easily change up to 25-30% of the water with no problem, maybe up to 50%. Make sure to let the water sit out in the room with the tank for at least a few hours, and if you are doing a larger water change, (50% or more) don't pour it all back in at once, do it in 3 or 4 batches. 15-30 minutes between each. That way, if there is a fluctuation in kH, gH, etc, you aren't replacing it all at once, and reduce shock to the beta, by doing it a little at a time.
To feeding, are you only feeding pellets? And what type/brand/size? I have only had a few bets in my life, and never seen any of them show much interest in pellets. Things that slowly float to the bottom, and drift, seem to do better. Frozen cubes (especially bloodworms) & flakes, etc, seem to do better from my experience. They seem to be clumsy feeders, needing things that "drift". For one Beta, frozen cubes probably wouldn't be economical. Unless you could cut them in half/thirds while still frozen. Maybe dried bloodworms, and a *high quality* flake food (I highlight that because there are a number of flake fish foods that are simply crap). To the filter/current, you might have too much flowthrough for your tank. I assume it isn't adjustable? You can always re-position it. Maybe put it towards the side of the tank, and aim it into the glass and slightly downwards to disperse the flow?
I didn't mean not to ever move the plants, what you don't want to do is just stir things up too much. You want to suck it up with the vac, to do that, it needs to be in the gravel until you get there with the vac. Just stirring the gravel up moving things puts it into the water column, makes it harder to catch it in the vac. Make sense?
