i just followed the svn instructions - basically download and compile then ran ./ufo from the trunk directory - does this count as "installing"?
no.
make install would have installed the game to the /usr/... dirs but it's not a must. I run it from the source too.
are you saying that doing this also sets up stuff in the hidden .ufoai directory that synaptic would use
Running the game creates the dir in your homedir to store your ufoai config, saves, screenshots. Both versions use the same directory.
as a matter of interest how do you tell what version you are running from within the game?
You mean which (svn) revision? If so, you can't.
You can query the revision of your svn checkout with
svn info command from ufoai sourcedir.
-geever