1- Say for right now I only have 1 internal drive (OS here) and 1 external eSATA drive, which drive would be better for my scratch disk? I've been pulling files onto the internal drive and encoding to the external drive.
I edit SD (please take note of this) on a very fast, capable laptop, and edit to/from FW-800's. I keep my entire Project, including my media Assets, on these, and swap to/from my workstation. In your case, eSATA will be even faster. While not the ideal, if one does not have multiple internals, it can work. As for AVCHD material, much will be directly dependent on your CPU - a lot of processing. Also, since both your OS (and its Page File), and your program are on your C:\, I'd give it a break and keep everything else on the external. Caveat: this is not the best solution, but a handful of fast, large internals is not an option for you. Now, I've got 3x 200GB SATA II's on my laptop, but still stick some of my Projects, completely, on my externals, just for portability.
I've never split the Scratch Disks over multiple FW-800's, though my controller has dual chips. Just never tried it. Remember, I'm doing what I do for portability.
2- If I am making a Blu ray disc (or really anything I suppose) how much am I gaining using VBR vs. CBR? If I encode with CBR with a bitrate as high or higher than the original AVCHD files am I going to have artifacting/macroblocking?
Do not do BD, so I cannot help.
3- This is more of a random trouble shooting issue but would there be any reason that I have some inconsistant encoding speeds? With the same settings on the same projects sometimes it flies and sometimes it crawls? This is on a computer where Vista 64 was installed on a freshly formatted drive just a few days ago.
First thing that I would look into would be running programs and Processes. Look at Task Manager (or another such app.) to see what Processes are loaded and drawing resources. One of the first things that I kill is Windows Indexing. It has to be set to OFF for each disk and do include ALL folders. Many, many other programs can zap your resources, causing all sorts of slowdowns.
I've been using 2 pass VBR but it takes so long I wanna know its worth it
In my tests with DV footage, 2 pass does not make any appreciable difference in the final output. All it does is add to the transcoding time.