What is best workflow from Premiere Pro to AFX for a template?

Hey guys,

So i bought a few After Effects templates from Videohive. So im editing small clips in Premiere Pro CC.
Id like to know what is the best method to import those clips in AFX for inserting into a template.

I find that the replace with after effects composition, is kind of messy. It creates all kinds of files
and folders into the template. Redering each of my edited clips one by one is too time consuming.

What is your workflow with AFX templates & editing in Premiere Pro?

Thanks in advance!