John,
You have obviously put a lot of time and effort into building what is a very realistic looking layout and as such I think you should seriously consider installing more prototypically correct signalling.
Unless your track layout is totally unrealistic (which I very much doubt) it will be possible to signal it as per the real thing using the basic rules of signalling. There are a number of books available on the subject and I'm sure that certain members of this forum will also be willing to help with any queries.
Here's one book that I can personally recommend.
http://www.amazon.co.uk/Modern-Signalling-Handbook-Stanley-Hall/dp/0711031436