If i understand the problem correctly it seems a possible solution would be to make
screen 2 the synergy Server ( and therefore screen 1). It seems like synergy intepretes the position in relation to the server.
EDIT: You can create or edit the synergy configuration file, which has several sections. In the section 'links' you can edit the relativ position of the screens to each other (as in edges). You can find a guide how to do this at http://synergy2.sourceforge.net/configuration.html
If you replace host1 with the correct names it should something like that:
down = host 2
up = host1
If host1 is your primary screen it should switch to it, and for your other monitor you dont need synergy anyway.
(Edited with my phone so sry for the formatting)