General time constraint questions

So far all the documentation on TQ only shows trivial examples in which all the entity names, paths + delays are very simple and already identified for you. In a real project the hard part seems to be understanding what (and where) TQ is complaining about so you can actually do something intelligent about it.

In my project, I've put in the base clocks and generated clocks statements, and now I have post-fit analysis showing many violations. Is there some preferred plan of attack?

Do I need to have all constraints in place before I worry about violations?

I don't understand most of what it is complaining about since the names are not part of my user logic. I see several setup violations which list a base clock name as the launch edge. Base clocks only go to plls. There shouldn't be any logic driven directly from base clocks. All the logic is driven from pll output clocks.

If I could fix even one problem I'd have some hope for this tool.