The ADI designs load the designs in this order-
base (depends on the carrier) (e.g. projects/common/zc706/zc706_system_bd.tcl)
fmc (depends on the target hardware) (e.g. projects/fmcomms2/common/fmcomms2_bd.tcl)
system (exceptions & tuning) (e.g. projects/fmcomms2/zc706/system_bd.tcl)
You can source these 2 board files in your poject (you don't even need to use our project tcl files). Then create a "customization tcl file" that will modify the design.
As an example let's say you would like to remove hdmi (this is for reference only- you have to find the proper TCL commands and use the right syntax).
delete_bd_objs [get_bd_cells hdmi*]
delete_bd_objs [get_bd_ports hdmi*]
You want to replace a DMA to VDMA
delete_bd_objs [get_bd_cells dma]
create_bd_cells .... vdma
set_property --- vdma
delete_bd_objs [get_nets old_dma2other_modules]
connect_bd_net [new_dma2other_modules]
This will be the easiest thing to do-- if you let the tool to generate the board files-- it will be a mess.