You may already know this, but I've seen MORE shift boots installed upside down than I have right side up, so I tend to make some noise about the right way to do it. My apology to you if you already know which is which.
The socket part of the boot is to seal road debris from getting near the fulcrum ball, and the upper portion of the boot is molded to seal tightly above/below the sheetmetal xmsn tunnel.
In the pic above, you can see that I used a ty-wrap around the shifter's cup, because while struggling to get it onto the trans tunnel, it's easy to pull it off the trans and harder to get back on.
[/soapbox]