Left eye. And I'm right handed. I understand the benefits of using the right eye, but it just doesn't work for me.
My natural tendency is to close my right eye. But if I do this too much, I end up with a sore eyes and a headache. Ultimately, the view from both eyes won't align for a period of time. No idea why. I have to consciously will myself to keep both eyes open.
This problem I had, too. Until I switched from a 40D to full-frame 5D MkII. The 7D has enough viewfinder magnification that it almost appears as a FF viewfinder, so no problem there.
5D3, 5D2, Sony α6000, G16 | EF: SY14/2.8, V20/3.5, 28/2.8 IS, Ʃ35/1.4, 50/1.8, Ʃ50/1.4 EX, 100/2.8L IS Macro, 16-35/4L IS, 24-105/4L IS, 70-200/2.8L IS II, 1.4x II, 2.0x III, 70-300L IS, T28-300 Di VC PZD, Ʃ150-600 DG OS HSM S | E: SY12/2, 35/1.8 OSS, 16-70 ZA OSS, 55-210 OSS, SY300/6.3 ED UMC CS