This one got me too. Still does a little bit even when I'm inserting my OWN clip files! Of course, it depends on what kind of clip files you're inserting. You should start by creating a new object similar to the one you're inserting. For instance, if you're inserting a cloud clip file, create a new cloud layer to see how the program sets them up itself in the node network and then bring your inserted nodes over and substitute them for the program created ones.
Personally, I'm not a big fan of the node network, but I understand why they use it, so I have had to teach myself enough of it to get by.