How to increase the capacity of APCs?

Upgrading the barracks building will increase your max capacity for an APC. Upgrading hero's skills will also let them have a higher capacity of units within an APC.

There are also research items under each APC and also under each troop type to increase their load capacity which will help, however the main factor is the troop numbers, upgrade the barracks buildings and level up the heroes skills as mentioned above to increase the number of troops in each APC.