Once you have the structure diagram on display you can flick off both particular CI types and particular relationship types from the display filters at the bottom right.
If you create a relationship that has the property 'unique' then that will prevent you from adding that in more than once.
So I'm not sure if that helps at all, but I thought I'd mention it.
hmm, I think the problem to make the relationship unique is that I will get thousands of unique relationships (one for each relation).
What I was thinking about was to have the 'to configuration item' dropdown filled with CIs which are unused.
I tried to create a filter just to show the e.g. software CIs which has not been used in a 'configuration item relationship' in the 'to configuration item' dropdown but I didn´t get that working