Let's make it short: Read the help. Seriously, all of your questions are basics and if you don't even know how to scale a layer, then there's not much point discussing anything else.
Sorry I do know how to apply a second video, move and resize it so its in the corner. That isn't too hard.
The biggest problem Im facing is having to extract the work area, tracking the camera for that segment that I wanted to add the 3D text, and then somehow being able to get back the rest of the video. I tried analyzing the whole video but it took a long time and it ended up failing. I move a lot in the shot and in the start, where Im stationary, is where I wanted to add the 3D text.
I did read the help and got the basics but I figured I could get a faster answer for what I'm trying to do on here.
If you want to track only a part of a shot just split the layer or make a separate comp with just the part of the shot you want to track. The work area has nothing to do with it. Split a layer at the CTI by pressing Shift + Ctrl/Cmnd + d.
To learn how to use AE start here: Basic AE. It will take you forever to figure out how it works if you just poke around and ask questions on forums. To explore specific topics like camera tracking just type camera tracking in the search help field at the top right corner of AE. It's you best and fastest way to get to the training you need. AE is not an app designed to be used by amateurs by giving them automated solution at the click of a button. AE is an app designed to give a visual effects and motion graphics professional the tools to successfully combine the sometimes hundreds of elements that are needed to create a 4 or 5 second composite. After Effects is not the right tool to edit your 10 second track into a 2 minute movie. You create your composite then you edit in Premiere Pro. Smart AE users do not process a single frame more than they need to in AE and they edit their story in Premiere Pro or their favorite NLE.