The FOTA Service can be used alongside with other custom services but it requires some modifications from the basic FOTA example.
The difference is that all attributes defined by all custom services (including FOTA) must be inserted into single attribute array that can be passed to the GATTM_AddAttributeDatabase function in one go.
As an example, this has been done in the firmware for the Lighting Kit platform which uses 3 custom services + FOTA service.
The source code for the platform is part of BDK CMSIS-Pack, example: Lighting Kit Firmware (FL7760, RTOS, FOTA).
The creation of attribute database is located in source/module/lk_ble_custom_attdb.c file.
Lighting Kit page+pack: Link