HOMER does not model the battery charge controller as a separate component. So you must include its cost and efficiency in the values you specify for other components.

If you are simulating a PV-battery system or a grid-connected PV system, the best place to include the charge controller costs and efficiency is the PV aray inputs. In the cost of the PV array, include the cost of the charge controller. Then reduce the PV derating factor to account for the efficiency of the charge controller. For example, if you want to use a derating factor of 90% to account for losses in the PV array, and the efficiency of the charge controller is 95%, then change the derating factor to 90% * 95% = 85.5%.