Vicki:

In my past experience (on the academic level) and now with my contact with
academic institutions as clients, I must say that yours is the number 1
concern:

HOW TO MAKE IT A CLEAR, CONCISE AND VIRTUALLY SEEMLESS process for the PI
 --  and still COMPLY with the regs.

The only singular answer is electronic routing.  Similar to using the forms
templates such as the NIH 398 for MSword... make your forms into electronic
templates with a routing procedure which is accomplished through your
electronic mail system.  If I am responsible for reviewing submissions to
the IRB prior to setting the agenda...  these submissions arrive as
electronic messages in my form template to a dedicated mailing address.  If
a modification must be made, it is much easier because the form is
electronic (I can mail it back in seconds -- with an attached note) or make
the change and send a copy to the PI.

Lisa F. Richman