Are you in a part of the country that receives a significant winter (ie., "USDA hardiness zone 5")? If you are I believe at this point your roses need to be preparing for that. I am in hardiness zone 6 and I don't fertilize after Labor Day. I want my roses to stop producing new growth and fertilizing them usually stimulates new growth more than anything else.

If your roses were more or less healthy this last summer I suspect at this point you mostly will want to be preparing them for winter. To me that would mean making certain they had enough water (supplemental irrigation if you aren't getting regular rain), but not much else until killing frosts were happening regularly, and then once those frosts were occurring I would add whatever extra mulch I was going to add around the canes.

Mathew,
It depends on how much work you want to do.
I have Fourth of July and the only thing I use for winter protection is oak leaves. I let them accumulate at the base of each bush and any I pick up with my lawn sweeper are put back in the beds around the roses.
My Fourth of July dies back to about 2-3 feet each winter but that's fine with me as it's a modern climber that blooms on new wood. Winter protection starts when planting your bush. In zone 5 the bud union (graft) should be planted 4-6 inches below the soil surface.
JFK is a tender hybrid tea. Even with good winter protection it'll die back to the ground or just plain die. Look into hardy shrub roses for continuous color all season and no winter protection worries.
In many cases, hardy means although a bush will die back it grows back strong by late May and will reward you with a nice spring bloom. In some cases, hardy means the bush will retain viable canes all winter.
All modern roses bloom on new wood so dieback is not all that bad. The important thing is to protect the roots and lower cane portions.
Wait until a good freeze, mulch well, and water if you have a dry fall. No fertilizers until just before they bloom next spring.
Where are you in zone 5?

Also, if you would, please, describe what you mean by "rust". Rust is a pretty specific disease, mostly on the west coast.

Were these new roses you planted this spring? If so you may want to mulch them heavily for their first winter. Contrary to popular opinion not all HT's are sissies either. With good winter protection your JFK will probably do fine. Mine does. If that 4th is new it will take a good 3 years before you'll see it really take off so be patient. You may only get a few blooms these first few years. You can wrap them with burlap for extra protection if you wish. It should protect more of the cane from drying out and dying back.

Zone 5: your already two/three weeks behind... Your get out of jail free card reads like this:
Stop all ferts just like York and Seil had said get a nice layer of alfala hay two - three inches deep at the base of all of your roses add to that layer as many of them fallen leaves as you can get walk around ontop of em for a couple minutes to hold em down as leaves fall add em on and walk on it again for but do this with fluffy not stuffy and about 6 inches high as a goal the rain helps hold em down so add more on as needed then wrap em in a burlap as an option yes but a better idea as well ty seil.

I don't think it's a matter of how much work you wanna do or not the less you do now is the more you'll have to do next yr and right now you need to do alot don't get lazy ok it will only pay off later. Listen to York and seil they know this wintering info as well as I do, trust us you don't wanna skip this step.

Hi York: Matt may of had alot of extra rain this past season just like you and I did perhaps even more his zone 5 says this... I'm sure he'll follow up and add his state. I think it's best we wait til later to help him on that rust problem.. agree ?
Pest probelms: I am 100 % organic matt think it over during the winter and make up your mind on that I say this as I will step on toes when other methods are used

Pre spring prep: this will make sence in spring but final steps are theres going to be some left over hay with a five gallon bucket and lid fill the bucket to half full with hay and let the rain fill it to 2/3 full then snap close the lid any remaining hay can be stored in a cool dry area garage, shed, basement, ect the base of it is going to stain the flooring or any surface you are not going to be able to clean this stain so a 1/2 inch piece of plywood will prevent this stain
leaves : find an area in the corner of your yard to place any left over fallen leaves this area is going to stain too think of it as a composting area it will need to be big enough to hold these leaves build em up has high as you can

Example my leaf storage area is 40 feet by 30 feet by 10 feet high late fall it shrinks to 0x0x0 by the end of spring and I end up hunting for more during summer AKA composting

enjoy the work Matt it's well worth it

Buy some bags of topsoil and keep them where the will not freeze (on a shelf in the garage). Around Christmastime when it gets real cold, mound some shovelfulls of topsoil on your tender roses. Remove protection when forsythias bloom in spring.

sorry I'm late getting back to this thread...i live near Saratoga NY. Yes we recieved record rainfall this summer. The "rust" I mentioned was exclusively on the 4th of July. I did actually transplant the 4th in the spring from one part of my yard to another. I used bone meal,peat moss and aged horse manure. ..Back to the rust..it seemed like the leaves were brown and withering on some parts of the plant.

The JFK was great this year. I used horse manure and miracle grow to fertilize throughout the summer.
Also both rose bushs are not new. They are both about 3 years old. I have plenty oak leaves and I plan on putting a bunch of them at the base of each plant