"...is it generally recommended to use the bars that fit into the
gutter, or to drill into the fibreglass and attach directly to the
poptop?..."

Jeff: No bars required -- foam blocks suffice.  Google search "canoe
on westfalia" to get some ideas.  One example:

http://www.google.ca/imgres?imgurl=http://www.westfalia.org/community/gallery/files/2/7/5/3/8/van-canoe.jpg&imgrefurl=http://www.westfalia.org/community/gallery/showimage.php?i%3D1108&h=450&w=600&sz=48&tbnid=My5IwTtyiFTJyM:&tbnh=90&tbnw=120&prev=/search%3Fq%3Dcanoe%2Bon%2Bwestfalia%26tbm%3Disch%26tbo%3Du&zoom=1&q=canoe+on+westfalia&usg=__elNOfuXmbwn1CpjdqcezgAzDPkk=&docid=q8iXpjtORH9CXM&hl=en&sa=X&ei=jgszUKHpHsfrygGW_4HIBw&ved=0CFAQ9QEwAg&dur=495

I would choose some other position for the foam blocks so that the
canoe is not touching the van directly.  Could consider letting one
end hang off the back of the van sufficiently so that the other end is
in the luggage hold.

Or could consider strapping a bar across the luggage hold to gain some
clearance or stability with the canoe resting on foam blocks at the
rear end of the pop top, depending on canoe length and beam.

gabby