I personally wouldn't build that unit the way you describe. It has a few drawbacks I try to avoid.
It will be a huge and extremely heavy unit. I'd be more inclined to build the cages seperately to make it easier to manage.
The main problem I would have with it is the height of the individual cages. Alot of people use very low cages, some down to 11" of height in a 4x2 cage. I personally don't like these dimensions. The finished cage looks odd to me being so short compared to the length and width, and I prefer a little more vertical space. I normally go 18" high for a 4x2 cage. It just looks better to me.
Granted, the vertical space isn't always needed, but it gives a better proportional look to the finished cage.
Cages that size are really an overkill for the species you intend to house in them. More space is always better, but there comes a point where there's just no need. Large cages like that are great however for naturalistic displays, but again the height would be a detracting factor from the finished look.
I would probably go with a 3x2x16 cage like
this one instead and heat it with 1 foot of 11" wide flexwatt.
I've been pondering a similar cage design for a while myself. I built one years ago, which needs replacing now, but it was quite basic and made entirely out of melamine. Since then I have not built many multi cage units, they're just more difficult for me to deal with in the herp room.
I've been thinking about a 4 cage unit for my son's bedroom to house his cornsnakes in, built similar to what you describe but smaller in scale. It's a little difficult to put into words what I picture in my mind though.
I'm currently constructing some cages that would be ideal for colubrids which incorporate a subterranean hide drawer in the cage which can double as a laying chamber for the females. This essentially doubles the area of the cage without extending the dimensions.
To answer your questions though, your best bet will probably be to put the flexwatt inside the cage. There's not alot of alternatives when using flexwatt in a wooden cage. Melamine is a great insulator, and that adds to the inability to put the tape under the floor.
When I install heat tape inside the cage I solder the connections and coat them with silicone to water proof them. I also silicone the flexwatt to the cage foor to prevent the snakes from hiding under it. It also makes cleaning easier since bedding and urates don't get under it either.
You will definately need a temperature controller of some sort. I haven't used the ESU controllers, so I don't know much about them. I have used Helix and Big Apple proportional controllers and both are nice units.
A proportional controller isn't absolutely required though, and they are fairly expensive. Colubrids just don't need +/- 0.5° accuracy. I am really fond of the ZooMed Repti-Temp 500R thermostats for a reliable and inexpensive controller. I use these on many cages and even my incubators. They are an on/off type and can be had for $22.50 from Reptile Direct, the cheapest place I have found for them.