These methods will allow you to play Roma Surrectum II while at the same time being able to play stock RTW.
METHOD 1
1: Download Roma Surrectum II and it's patch.
2: Download JSGME.
3: Create 'MODS' folder in your R:TW folder.
4: Install JSGME in your R:TW folder.
5: Install Roma Surrectum II and it's patch in the MODS folder.
6: Enable mods with JSGME.
You can now easily disable Roma Surrectum II if you wish simply by disabling it in JSGME.
METHOD 2:
1: Download Roma Surrectum II and it's patch
2: Copy your R:TW folder.
3: Paste it in a new location (I used C:/Total War Central)
4: Rename the copy 'Roma Surrectum II'.
5: Install Roma Surrectum II and it's patch using the installer provided by the mod team.
METHOD 3:
1: Download Roma Surrectum II and it's patch
2: Download JSGME.
3: Copy your R:TW folder.
4: Paste it in a new location (I used C:/Total War Central)
5: Rename the copy 'Roma Surrectum II'.
6: Install JSGME in your Roma Surrectum II folder.
7: Create 'MODS' folder in your Roma Surrectum II folder.
8: Install Roma Surrectum II and it's patch in the MODS folder.
9: Enable mods with JSGME.
You now have two installs of Rome: Total War. One with the stock game, the other with Roma Surrectum II. If you use Steam, use the Roma Surrectum II launcher as usual. You may also want to link it to Steam.
I would personally recommend method 3, but it's your call.
Thank you to the creators and benefactors of Roma Surrectum II and to the creator of JSGME (wherever you are now).