The easiest way is to first start the FEATool toolbox GUI, and then leave it open in the background.
Alternatively, you can manually add the searchpaths to the running Matlab instance.
addpath(genpath('path_to_toolbox_folder'))
where "path_to_toolbox_folder" is the
App Path: shown when you select "System Info..." from the "Help" menu in the toolbox GUI. If you want to make this permanent, you can use the
savepath command.