Retroarch - Setting the refresh rate?

[vrada501]

I've had a CRT-Emudriver set up going with my NTSC Sony Wega CRT TV and am able to run emulators at the consoles native resolution. I've been trying out different emulators,
got into Retro Arch and while I'm still a little new to it, I found that made it easy to run SNES emulators without scaling issues.
I still have a quick question though about the refresh rate setting...

Are you supposed to set it to the refresh rate of the console (example, SNES I heard ran at 60.098 (and I've had it set to that)), or to the refresh rate of the current modeline installed with VMM maker under CRT_Emudriver, or to the refresh rate of the CRT?

While I've had it set to 60.098 for SNES business, it seemed *almost* perfect to me, though there are moments where I feel like I noticed a very little tiny visual lag.
What other settings should I be worried about when trying to the most accurate refresh rate? I would appreciate any other advice involving this if there is any.

Thank you for your time reading, hope to see helpful replies. If it helps it's on Windows 7 64-bit.