I can't say anything about the size of the pot without knowing how big the tree is. I don't think that filling the bottom with water bottles is a very good idea, though. It's bad for drainage. If you need it in a smaller container, you should really use a smaller container and not try to modify a big one.

Citrus love nitrogen, and Holly Tone (actually all those "tones") doesn't have enough. I wouldn't modify anything now, though. It's pretty late in the year and getting to be time to give our plants a last dose of fertilizer before winter. If your tree looks healthy, I wouldn't fiddle with fertilizer changes until spring.

Even a dwarfed citrus tree can get to be 20 feet tall if you don't prune it, so you should definitely prune it sooner or later. The easiest way to prune is just pinch off the green sprouts as they come out, but there's nothing wrong with using clippers. The best time to prune (if you need to use clippers) is also the spring. You should definitely plan to clear out any in-growing branches and any branches that cross each other, and if you have more than 2 branches growing from any one spot you should trim them down until there is only 1 or 2. You can prune for height at the same time, to keep the tree a manageable size.

If I may ask, what zone are you in? And what kind of potting mix are you using?

its almost 2ft tall and very bush andthick