Is your stock actually 5.5 x 8.5? If it is you will have to setup your printer
for this custom size. (portrait) Set your margins at .25 side, 1 inch top and
bottom, grid guide, two rows, .5 spacing. Or 1.25 top and bottom margins, zero
spacing in the grid guide. This is assuming of course you are wanting the
standard 5 x 3 index cards.
The above is if you are starting from scratch.
Did you obtain an already perforated card stock? It would be helpful to know all
the nitty details, such as what version Publisher.