How can I combine two switches on two circuits on 1 timer switch?
Since you have two circuits (i.e. two home runs from the electrical panel) in play here, you can't "combine" the switches in the manner you're thinking of.  This leaves you with two options:


You can buy a second RPLS540A EconoSwitch and install it in place of one of the 3-way switches for the outdoor lights as per the instructions.  This is the simplest approach, but leaves you with two EconoSwitches to program and the possibility that your two sets of lights will wind up "out of sync".
If you have a neutral in the box for the single pole EconoSwitch, this also raises the possibility of a setup using a SPDT relay in place of one of the three-way switches with its coil controlled by the existing EconoSwitch; this would require running an extra cable from the box with the single pole switch to the box with the three-way switch for the outdoor lights, though.  You would also need to swap the existing EconoSwitch for a RPLS740B: the RPLS540A you have passes the power it uses to operate through the load, while the RPLS740B uses a neutral wire of its own to get its operating electricity "back home", so to speak.