For argument sake and ease of reference I will number strings from 1 - 6. 1 is the thinnest 6 being the fatty.

First things first, my build.. 

I don't think about scale length, I go for aesthetics. Small box, shorter length. Big box longer neck. I will work out fret placement and scale length near the end of my build. 

So let's say I have a small box and short scale. I know that a high pitch will suit that build better so I grab 1 2 and 4 

Nice big box and long neck 6 4 and 3 

Small box and long neck I hit it somewhere high say 2 3 and 5

As you can see, my box size is my biggest factor but I do consider my neck length. All of these choices are rudimentary at this time and may change later. I skip a string because I know that if I don't then this 'bass' string will feel flabby and personally I want it to be nice and tight. I know that my high string won't be at maximum tension because it suits my playing style for fast riffs if it sits a little slacker than normal.

So my strings are on and they are all wobbly. So I pull them all up about 3/4 and still out of tune just so that I get good tension on the neck.

It's about then that I begin to play around with the feel of the strings, the flexibility between the thinnest and thickest string both being pulled up in scale together and both being tuned to the same note but an octave apart. Also when I'm doing this I roughly bring up the middle string but I don't concern myself if it's a note out. I chase the high string with the low string up until I get it nice and comfortable on my fingers. 

What? No tuner? .. Well, no. I don't worry about it being in concert pitch. I just want it to feel good first and foremost. Of course I want a forth and a fifth harmony between the strings because this is my standard tuning style for my standard CBG. But it's mostly the feel of the thing I want. It's also about now I consider switching strings depending on how the box sounds with these strings. Maybe this particular box might vibrate better at a different range of frequencies than my initial choice. But for argument sake I will stick with these strings.

It's about this time that I fiddle about with it going up and down a tone or two to get a nice ballance of tension between all three strings. Only then will I reach for my tuner to get a concert pitch. Whatever notes I have on it stays on it and it's only a matter of going up or down by at most 1/4 tone. That particular guitar now has its own tuning balanced between how it sounds and how playable it is.

Don't get me wrong, I do have a standard CBG that I force tune to whichever pitch of song I'm learning to play at that time but it is on this instrument that I am most likely to break strings with and find fingering and string bending tiresome.

The important thing to remember is that because the tuning between the strings is always a fourth and a fifth for a standard CBG then it doesn't matter which pitch this or that guitar is currently in. The finger placements for any particular song will be the same.

I hope this all makes sense and please forgive me for using the words standard and CBG in the same sentence.