Do you mean how to choose the mouse protocol on text mode (using gpm) or X? Both have different configurations.
In case of gpm (text mode) you could run: gpm -t help | less
That will list all support protocols and then you can edit the correspnding line in /etc/rc.d/rc.gpm (I think that's what pkgtool does).
To configure X, you've to edit the /etc/X11/xorg.conf file as datadriven said and choose the protocol there. You can find about different protocols here: http://www.x.org/X11R6.8.2/doc/mouse.html
Most configurations will work with IMPS/2 or ExplorerPS/2 protocols.
It's known that sometimes gpm can conflict in X, so you could try stopping it with: /etc/rc.d/rc.gpm stop
And try to see if X behaves correctly.
Regarding the psmouse module, I don't have the original kernel in my machines, but maybe it's compiled directly into the kernel and not as module.