Hi mate, have you seen the instructions on mkiv.com, they're excellent and I used these along with the insructions that came with the controller to install mine, and I had no experience of these things at all.
I'll try and paste the link below, hope it works, also, I assume your referring to the Apex'i AVC-R.
The link may only go to the main index in which case you'll nedd to select Tech Articles from the list on the left and then scroll down to Section 3 - Bosst Control
http://www.mkiv.com/main/index.html
As far as capping off is concerned, I used about an inch of the supplied hose and bunged up the end of it with some rubber plugs I happend to have with some super glue to secure.
Also, don't forget to disconnect the electrical connection to the original vsv, I did and caused a very strange boost pattern, turbo 2 would slam on instead of bossting up gradually.