If you bottom water, put the pot in a bowl or tray with water up to at least half an inch up into the soil (ideally a bit more) and wait 20-30 minutes, then move it to an empty saucer or tray and give it plenty of time to drain. It should not be sitting in standing water afterwards. In my experience bottom watering and top watering yield roughly the same result, so there is no particular advantage to one or the other (except convenience) most of the time. I do bottom watering for my baby seedlings because they are really easy to dislodge with a drop of water landing from above.
What I would recommend is watering well from above, then waiting a few minutes and returning later to water some more, thus saturating the soil. There is no advantage to watering short of saturation, especially in an unglazed clay pot. To avoid root complications, just wait until the soil has gone dry at depth before watering again. This should happen in relatively short order in an unglazed clay pot, since the soil will evaporate through the sides of the pot as well as the top, especially given strong light and warm temperatures. It will happen later than when the surface layer dries out. Try poking your finger in an inch or two to get a sense of when the soil is going dry.
Strong light will help with watering, as will good air flow, warm temperatures, and good drainage. When in doubt, wait to water. However, there is no advantage to allowing the soil to remain bone dry for any extended period. Just try to allow the soil to dry and you should be rot-free.