Sure, it can work.
Many of us have multiple versions of Linux installed. If you plan ahead, you can even have multiple version of Linux on the same hard disk. I have five different versions of Linux on my computer (mostly for testing other versions).
But the standard warnings for installing just about any version of Linux apply. You should have your data backed up before you start installing. The partitioning part of Sabayon's installation appears the same as most other versions of Linux that I have installed. You will need to select the partitioning options that install Sabayon to the hda disk and leave the hdb disk alone. They try to make this as straight-forward as possible, but even intermediate/advanced users occasionally have an "oops" here.
So there is no reason that installing SabayonLinux to your hda disk shouldn't work just fine, but you should always be ready for bumps in the road.
Gigabyte GA-P35-DS3L - Intel(R) Core(TM)2 Duo CPU E6750@ 2.66GHz
nVidia GeForce 7600 GS
2 GB RAM