I used to bend the antenna down and tuck it into the edge of the latch on the saddlebag, then I cut the antenna down to 24" Most folks swap out their antennas for the stubbies.
hello, On mine I figured out were the antennas would go thru and I put small grommets thru the cover and they go over the antennas so they stick out of the cover.
Both of the HD covers I own (the one I bought for my RKC and the one that came with the Ultra) have a slit in the back that is velcroed together - the antennas fit nicely through this slit and the velcro tightens up right around them... but I also recently replaced both of the long whip antennas with the short stubby ones - I don't use the CB or Satellite radio anyway - with no apparent hit to FM radio performance - with these guys on the cover goes right over with no issues.