Exactly this method I'm already using since a long time in my plugins. When you load a position (FEN/EPD) in WinBoard or Arena, the plugin converts it into a board position, and then sends it to the engine - if this is done via direct RAM write or via the buttons depends on the engine (and how complicated each of these methods would be). Speed is no problem, because I switch to 'turbo' mode in the emulation during the setup.