The board looks nice. Good work!
Now, as for how to wire thing this is kind of depends. To my mind the whole idea of making your own board is all about making it the way you like and so it makes your PERSONAL guitar playing life easier and more pleasant, sort of speak. I was myself about starting building a board, but never got actually into it as I still am not sure how exactly I want it to be. It has to be custom all around, and custom means NOT! universal

. See what I mean.?
I've made up a diagram for you (attached), which shows you the basic idea about how I would approach the "system". This is only the basic idea. It's easier to draw a sketch that to type words about this stuff.
Couple points:
1. I would put the switching "system" into metal box, that's for sure.
2. Next you need to be careful about how to actually wire it.
3. I would add LEDs for bypass switches, showing you what's "IN" and what's "OUT". To add leds would mean to be using "tripple" two position switches.
Here's eBay links to someone who sells this stuff, I am not sure about prices, though, you may find them somewhere cheaper:
link:
http://cgi.ebay.com/3PDT-SWITCHES-TRUE-BYPASS-NEW-EFFECTS-BOUTIQUE-ROHS_W0QQitemZ200308436663
If you really don't care about LEDs, then you need this kind switches, link:
http://cgi.ebay.com/DPDT-FOOTSWITCH-TRUE-BYBASS-EFFECTS-WAH-PEDALS-NEW_W0QQitemZ200308435069QQihZ010
, btw, that seller got all sorts of parts for guitar/pedals and such projects, prices looks ok to me, but not really "sockingly cheap" ..heh heh
You sure can either have IN/OUT jacks for the pedals, or have short cables with TR plugs comming from the box. I would build a custom box, I would go for short cables with plugs and no jacks (less purts overall and the same result).
I have no clue where to find the metal enclosure that is ready to go and fits your design. I would make something up from crap-scap pieces, that's the way I make 90% of my "gear"

Re-use something
Good luck with your projects. Keep posting.
Here's diagram. Ask a specific questinon, if any.