Now what do I do?

Hi everyone and thank you in advance to responding to my thread.
We have had Gizmo for about a year now. He showed up at our door looking for a new home, and being the suckers that we are, we took him in. He's a wonderful little kitty, about two years old. He mostly likes to be outside, but he comes in at night and for various periods throughout the day.
In November, we accepted Charlie into our home. (He showed up at my brother's house, but he couldn't keep him because he already has four pets.) Charlie was an intact male, so we had him neutered immediately. We believed the testosterone would fade rather quickly because he seems to be only about two.
Charlie is a very aggressive fellow. He tries to attack the various neighborhood cats through the glass door. He actually succeeded in chasing away the neighborhood alpha male even though the glass was between them! When Gizmo comes in Charlie goes right for him, no holds barred. We have had to keep them completely separated. This means that when Gizmo comes in, Charlie gets sent to the back of the house. I believe this is only making matters worse, but I don't know what to do.
I have tried letting them get to know each other though the door and by seeing each other at a distance. We've tried giving them treats when things are going well between them. We've tried leaving a sock with Gizmo's scent all over it on the bed when we sleep at night (Charlie sleeps with us all night), but none of this is working.
Last night they ended up in the same room. Since no fighting ensued, we deciced to leave them alone and see what happened. It seemed to work out okay and Charlie left Gizmo alone. After Gizmo went outside, Charlie peed on the couch! He never did anything like that before.
This morning we tried them in the same room again but quickly had to put Charlie in the back as he went straight for Gizmo. Then Gizmo sprayed the ottoman! That has definitely never happened. Luckily, the furniture is leather... ugly but convenient.:p
I have two cat behavior books and I've looked for answers on several cat sites, but nothing seems to address our particular problem. They all seem to tell me what I should have done to prevent the problem and none tell what I can do for damage control. Help! Sorry this got so long, but I'm trying to give as much information as I can. Thanks!