How to create a template so each new video clip can be dropped in to replace the previous video

I've got my intial sequence for a daily video set up exactly how I want it; logos, titles, music with a thumbnail (a still taken from the beginning of the clip) all dissolving into the start of the clip. And then all the same disolving in and out at the end of the sequence. Each day I want to have everything the same but just replace the thumbnail/video clip with new ones.  Not sure how to replace them without messing up the rest of it. 

Also, sometimes the thumbnail/video clips are shot on green screen, so in those cases I also have a background. The background, under the green screen clip splits the audio away and then I run into problems when I try to drop the new video on to replace the old video.  Everything seems to get screwed up. 

Am I supposed to do a separate sequence for the greenscreen/backround layer and then drop that in as one whole clip into the sequence with my "template."  If so, I could use some tips on that as well.  It seems like a lot of extra steps.  

Thank you.