Just as in add_edge(1,2,graph) you get to choose the numbers which represent the vertex is it possible to do the same with add_vertex where i actually choose the vertex number. I guess the syntax might be like add_vertex(3,graph)

Directly using integers as vertex or edge descriptors not a good idea - it only works for some kinds of graphs. Also, add_vertex(3, graph) is probably not setting an index for the new vertex since vertex indices - those values indicate the position of the index within a vector (assuming your graph stores vertices in a vector).

Again, I'm not sure what problem this is addressing - it's hard to see what you're trying to do without a little code.