Is there away to modify countries in the base game to fit in with a mod (national focus,ideology,national spirits)

What do you mean by this?

is there a way that you can import focus trees or national ideas from countries in the base game into the site to edit and change 

also im still unsure how you set a national spirit to appear at the start of the game without a focus because iv read that you have orginal_tag = TAG in allowed but iv done that and its never worked 

You will want to create a new focus/ideas group/etc. on the site first.

Then, when editing, if you press the "Import" button on the sidebar it will allow you to upload the necessary file(s). If you hover over the info icons (i) it will tell you where to look for the files (based on default Windows install) if you're unsure which file you need.