I am assuming that you have Ultegra 6700 with the hidden cables.
Yes they are a ***** to change out.
I strongly advise against trying to disassemble the lever. Not only is it not user serviceable, it is not even shop serviceable. There are scores of tiny parts in that thing.
I am also assuming that you are probably putting on Hudz or something.
The easiest way to replace the hoods are to remove both brake and derailleur cables, then take the lever off the bars. Pull the hood over the front knob then back off the palm rest part of the lever. It is very difficult to pull them off over the knob and then down over the shifter paddle and brake lever. Heating it first will make the job easier. A couple minutes with a hair dryer on high heat may help. Also before installing the new hood, drop it in a pot of very hot water for a few minutes.
Before you attack the cables though, download the Shimano tech documents for the front and rear derailleurs, the brakes and the STI levers from their website.
http://techdocs.shimano.com/techdocs/index.jsp While they are not difficult to set up, the tech sheets should be referred to in doing so.
As to feeding the rear brake cable through the top tube of your Madone. Remove the rear grommet on the frame. (The one on top left side near the seat mast.) Pretty sure you need a T-10 torx driver for that. But a 3/32 hex allen wrench works too. With the grommet gone it is very easy to feed the cable back through and fish it out of the hole.
HTH
zac