Would a 3x3" piece be too small / large?
It depends on the amount of heat you want to dissipate. Heat sinks are defined by their thermal resistance, in degrees per watt. This means that for a heatsink with a thermal resistance of say 10o
C/W for every watt you dissipate you get a 10o
C rise in temperature.
See this link:-http://www.thebox.myzen.co.uk/Tutorial/Power.html
Also they are defined in 'free air' the effectiveness goes up with forced air and down if it is restricted. You want as much natural air circulation as you can get.
In order to see what thermal resistance you need and hence what size it has to be then you need to know what power you will dissipate and how hot you want to let it go.
Should I make two layers
No there is no point, as I said it is down to area not thickness.
and attach them with something like silicone adhesive
If you make a multi piece heat sink to get more area then bolt the pieces together and use heat sink compound between the pieces. Aslo use this compound between the piece and the component.