To be honest, I highly doubt you can actually control where the partitions are laid out much these days. The way drives lie about the geometry, how they optimize themselves with disk layout... okay, so yeah you still need to defrag (but that is a different, yet related problem)...
I suppose if you make two partitions on a drive... the first one is likely to be the 'inner' partition... and may be somewhat faster, due to the way seek times and latency works though, I doubt you'd see much of a performance boost.
Since I believe Win98... the OS has been able to defrag your system so that all executables are put in the 'fastest' area of the drive, where ever that may be. I believe the tech was listened from Intel a while ago or something, but my 'old' brain isn't remembering quite as well as it used to.
So my personal suggestion would be... keep your apps on your notebook drive... leave plenty of space for copying projects over as you see fit...
but keep the bulk of your data on your external drive...
Most likely you won't need to defrag your external drive often, but I would suggest defragging your notebook drive as soon as you are finished installing your apps, as windows likes to leave crap all over the place when it is installing software.