Woodworking in Home: Face Frame with biscuits tip

So, while I was building an E-desk (more on this later) I made a sort of rookie mistake with face frames and biscuits. I guess its not really a rookie mistake, I just was not paying attention and thinking of things before I was doing them. Anychoices, I wanted to use face frame biscuits to attach the rails to the stiles; for some reason I think pocket screws, although great, or just too much for this - I might re-think that. Anychoices, in this first picture you can see Ive laid out the lines for where I want biscuits to go; I like to put my two stiles together and lay out the lines together to avoid errors while transferring lines. You can also see in this picture that Ive cut the biscuits too, but I will show you what I did wrong.
Ok, it may be a bit hard to see, but this is how I laid the pieces out when I cut them with the biscuit jointer; can you see what I did wrong? Basically, I cut them from the same side, not opposite sides. What I mean by this is, I cut them out as I laid them out; what I needed to do was to flip one of the stiles end for end like in this picture.

From E-Workbench

If you can see in this one, my slots are now offset. Why is this the right choice? Unless you have your jointer set to cut perfectly in the center of the board, you will, if you cut from the same reference side on both pieces, end up with an offset of your rail to stile however much your bit is off of center. See picture:

From E-Workbench

This maybe isnt even a 1/16th of an inch off, but its off and not easily fixed without causing other problems.
What you need to do, if you are using biscuits, is to mark the outter face on all your rails and stiles. This will help you understand to what reference point you need to put the fence of your biscuit jointer. In my example here, becuase I was cutting them as I laid them out, I was then putting the biscuit jointer fence on the face of one stile, then on the BACK of the other stile, causeing the offset. If I would have marked the face on both of them, and cut from that as a reference, then I would have been fine. Make sense? So, mark all of the faces of your rails and stiles and use that as the reference point for cutting all of your slots. I eventually got it figured out by doing another piece and got it attached.