if you use a seperate power source for the motors than the one coming from the board, should you connect the gnd pins of the l293 differently ?
No see:-
http://www.thebox.myzen.co.uk/Tutorial/Power.html
and it is in that case still necessary to protect the board from voltage spikes with a capacitator ?
Always a good idea, see:- http://www.thebox.myzen.co.uk/Tutorial/De-coupling.html
and while you are at it:-
http://www.thebox.myzen.co.uk/Workshop/Motors_1.html