With 3 gallon you'll be watering more often. I would say 5 gallon. Make sure you have good drainage. Any soil-less media you choose should be fine.. but i would say not to do perlite only or some other type of passive hydro setup unless you really know what you're doing.
Roots Organics soilless would be good. test some feeding schedules and see what works. Consider incorporating nutrients with minerals and trace elements and remember to feed the microbes. If you use fertilizers that have a lot of salts you might build up too many salts and the nutrients will become locked. Test your PH levels regularly. As far as topping goes, you said you have indicas let them go 4 internodes from seed then top. let those tops go 2 more internodes and top. from there you'll start to see the final shape of the plant, take your cuttings and keep your plant in check. After a while you'll need to trim the root ball. This is simple enough and there's many tutorials on that. Use the search box and search for mother plants. Read what others have done and what worked for them and take notes. What genetics are you using?
