By default BOINC uses only the best GPU of its kind if there are multiple available. You need to set an option in config file to make BOINC use all GPUs.

First lets prime the config file. Open Manager and in Advanced View select Options -> Event Log options. Untick one of the checkboxes and click OK. Then go back, tick the same checkbox and click OK. This creates cc_config.xml file in BOINC's data directory.

Next open c:\ProgramData\BOINC\cc_config.xml with Notepad (if you have moved BOINC's data directory somewhere else adjust as necessary). Find the part that says:

<use_all_gpus>0</use_all_gpus>

and change 0 to 1 and save. Then restart BOINC.