When using a VPA (Variable-Pitch Connector) to connect roof rafters to a top plate, how and where do you install hurricane ties?
It depends. VPA’s have an uplift value and unless you live in an extreme high wind area, you probably don’t need an additional holddown. 

As you can see from Simpson’s product load table, VPA’s have an uplift value of 255 lbs. for Douglas Fir / Southern Pine and 220 lbs. for Spruce and Hem-Fir. See here: https://www.strongtie.com/raftertowallconnectors_solidsawnlumberconnectors/vpa_connect/p/vpa

Likewise, a standard hurricane tie like H1 allows 480 for DF/SP and 420 for SPF, as seen here. 

https://www.strongtie.com/hurricanetiesforplatedtruss_trusstiedowns/h-tsp_productgroup_wcc/p/h.tsp

If higher uplift loads are required, I’d use a “twist strap” with VPA’s.