I will create about 3 - 4 different tables for my site, each with totally different styling. Does it matter if I place all the override code in "ATO->Style tables -> Table Style" and "ATO->Style Tables -> Table body cells" or in "ATO->Add HTML/CSS inserts"? Thanks in advance.

I would probably style in the Table Style section but you could certainly clear out all the entries in that area and use CSS in CSS Inserts. Both will work.