Just in case you haven't sorted it already...
It's not very clear, but the pannier frame mounting points at the indicators should be inside the bike's subframe. Remove the bolt holding the indicator. Use a new bolt (I can't remember if this was in the kit) from the *inside*, that goes through the pannier frame, through the nut welded to the subframe, then through the indicator mount. Use a new nut on the outside to secure the indicator.
The other four mounting points under the seat and rack are quite simple. Remove the seat and rack, position the pannier frame on the bike (I usually loosely fit the footrest bolts), and then use the supplied longer bolts. The spacers are for the rear mounts of the plastic rack. They effectively level the rack due to sandwiching the pannier frame under the front mounts of the rack.
Hope this helps.