As Tim says, double routing the inputs to the second layer is a great way to keep the FOH dynamics and eq out of the monitors. It's almost like you get a free monitor board and splitter with each LS9.
There is also another way which is simpler, but less powerful. On the "mix bus setup" screen you can set pairs of mixes to be "Vari Pre-eq" This will make the pre-fade source for those Aux sends come from just before the EQ, after the HPF. This arrangement is similar to many internal jumpers in analog sound boards which allow you to change the source of the Pre-Fade aux sends. This method might be better, depending on what you are used to, and how familiar you are with the LS9 and the use of layers. Of course you will lose the ability to use channel eq and dynamics in the monitors.
When I first got the board I was all gung ho to use the dual layers for monitors. I was OK with it, but not great. I went back to the easier method while I got my head around using the board. Now I have switched back to the dual layer scenario.