The only reason to sight in the EOTech and then the BUIS is that the anytime you put something between your BUIS, there is a chance that it will affect the alignment due to parallax. Now with a non-magnifying optic (such as the EOTech), you shouldn't have any light refraction. However, if you're anal about your sights, you should sight in the BUIS with the EOTech on the weapon. That doesn't mean that you have you have to sight it in first, but you may as well sight in the BUIS through the EOTech.
That may be paranoid, but it will avoid any potential change in your BUIS alignment.
MickeyC, you're right about it being zero-parallax. The word I meant was refraction. Parallax is an issue caused by motion or movement of the point of observation. Refraction will occur any time that light passes from one medium to another (like air into the lens of an EOTech and then back to air). Because the light travels from one medium into another then back to the first, the difference is minimal (because it re-refracts). This is especially true for perpendicular light passing through the mediums. However, this is minimal, and I don't think it would affect the zero of the BUIS.
However, it doesn't hurt to sight in the BUIS in the same manner that you would be using them. Since you would use your BUIS through your EOTech (should it fail), it makes sense to me to sight them in that way. I guess that's my personal preference, but it eliminates any potential issues, however small they may be.
Given the effective range of the cartridge/rifle combination and the accuracy capability, it really isn't going to matter one bit which you do first. I just find that I group better by setting my BUIS first and then bringing the EOTECH in to match.