I think he means putting them through the lower piece of the bracket. I am looking at the photos on FR's website and it seems that you can throw away everything but the lower horizontal piece that goes under the rack itself. If the holes are too small for the Alpha bolts, just drill the hole a bit larger.
Either way -agreeing with FishinCrzy- you need to set the tent on the roof rack, and then add the bracket from the bottom, so that it goes around the slat of the roof rack. The lower brackets of the tent were pretty wide, so maybe it is worth to have a second look at the width of the roof rack slats and if they fit into the bracket that was shipped with the tent before you spent more money on the FR brackets (and use just pieces of it).
I have the Alpha 2 and added some security brackets (from
wheeleveryweekend.com), and the Alpha rails are a bit wide, so I used the Alpha bolts and brackets and added the two security brackets in addition to this - for those I had to grind down the heads of the M8s to have a washer fit into the channel to make up for the width of the channels (my roof rack has three horizontal bars, so the tent is secured in three places). However, the bolts that came with the tent carry the majority of the work, because the channel material is a bit soft and regular bolts will add too much pressure/bend the channel easily
.
