Let's see if I can describe this right.
If your roller furler system has all its parts, your forestay should consist of two pieces, an upper and lower. They're connected together with a swivel and a sheave assembly. The furler drum at the bottom connects to the lower forestay and the bridle wires. We'll assume all that is in place?
Ok, your jib halyard is also more than one piece. There should be a detachable part of it, connected to the rest with a "sister clip". With the jib not on, the halyard should be through the upper swivel sheave, with both ends able to reach you on the ground. Tip: I tie a small bowline in the end of the halyard, and hook it in the small shackle forming a big loop, that way you can't accidentally pull the shackle out of reach.
Now, hook the shackle to the top of the jib, and when you fix the luff zipper around the forestay, make sure that the part of the halyard you're pulling on is inside the zipper. Pull and zip, pull and zip. Hook the jib tack to the furler with a shackle. When you have the jib up, you've got a ton of extra jib halyard laying on your feet. That's when you detach the extra length by undoing the sister clips. Now you've got a much shorter tail to work with. Run it down, through the shackle, back up to the little block on the halyard (you've got one of those, right?), back down, and hook it into the clam cleat on the sail. I then wrap the rest around the halyard loops and tie it on itself. Zip the zipper the rest of the way down. Do all this, and the tail of the halyard should be clear of the furler.
If your halyard is all one piece, with no detachable part, you've got an awful lot of line to stow to keep it out of the furler. If you don't have the little block, it might not make sense how you can tie it off at all.
So, look at your halyard, make sure it has the bits I mentioned. If not, maybe you can order a new one from Hobie, or improvise. Go to the Hobie cat site, they have their catalog and parts lists online.
Good luck!
