Having trouble joining two edges I'm still a beginner and decided to model a lightsaber from a CG GEEK tutorial linked here.

I've been having some trouble joining two faces after running into trouble from double vertices in my mesh. I noticed it when I applied a subdivision surface and I've been having trouble solving it. The biggest detail that I've noticed is that the new vertices that were created when I tried to fill in the gap with the fill tool, aren't recognized as a face by Blender. Thank you for your advice.
Don't use the fill tool. Delete that big and ugly n-gon shown in the pictures, then select the edge loops you want to join (&#9095; Alt+ RMB), and press the space bar and type Bridge Edge loops



Read: How to connect vertices in a mesh efficiently?. 

Then, if you are using a subsurf modifier you need to select the edges you want to make sharp and crease them. Press &#8679; Shift+E and set the edge crease to a valud of 1.0

read: Keep sharp edges when using subdivision surface