Thank you Dr Jeckyll, I think your point is very valid about flicking through to the appendices to see the graphs, much easier in the text. Blue also has a good idea with the key graphs in the text and the remainder in the appendices as the number of them is too large.
For ch 3, I think I may have key graphs in the text but the remainder in the appendices (in order for ease). That way I can add the graphs for ch 4, 5 and 6 in the text. Therefore some consistency is acheived across the chapters. I also have tables in all chapters so added to 60 graphs is an illustration overload in ch 2!
I am finding the graph annotation, numbering and insertion a tedious job and just want to get it right first time. I don't relish having to go back and redo this part. I am getting so near to finalising the thesis but still lots to do......ok relaxing now :-)