Sanbeko,
Universe Sandbox is certainly capable of running simulations similar to what you've describe. Although the creation tools for new solar systems are admittedly weak and data analisys tools are missing altogether.
I would describe Universe Sandbox as a representative simulator and not something that you should use to launch rockets to other planets or base scientific work upon.
Create new systems is fairly straightforward by editing the XML system/simulation files, but it doesn't currently have any way of graphing data so any conclusions about stability would be from visual observation.
You should check out
Gravity Simulator by Tony:
http://www.orbitsimulator.com/It has the ability to rotating frame and exporting the results of simulations for graphing. It also has an export feature so any simulations you create can be visualized with Universe Sandbox.