I believe console players stack items in the guild bank by withdrawing them from the guild bank, then putting them in their personal bank, withdrawing them (now stacked appropriately) back into their inventory, and then finally putting them back in the guild bank. It sounds like a huge pain and if you have guild officers, I'd get them to help you.
This is one of the main quality of life issues I'm shocked ZOS hasn't fixed since PC launch. At least we can drag and drop, I pity you guys on console.