The male of the Y cable plugs into your Guitar
The Two females of the Y cable just have regular male to male leads each running to an amp - any arrangement like this will tend to decrease the available signal - i.e. the weak signal from your guitar will be split between the two amps and distortion may increase accordingly.
Also; if there's a wiring fault in either of the amps, by connecting the Amps together through the Y cable it may cause other problems and could jeopardise safety especially if there's a bad earth in the set up.
Take care...
Peccavi
March 2009