If you /must/ use the FL lens on an AE-1.. From what I can tell it appears the camera thinks the lens is at f5.6 (no matter what it actually is). This is surprisingly convenient because the range for the needle centers on f5.6!
So in use, I think this is the way to do it: start with the lens wide open and adjust the shutter speed until the meter needle centers (on f5.6). Then shoot! if you want to over-expose, adjust the shutter speed so the needle is physically higher (at f8, 11, etc) and leave the lens wide open. If you want to under-expose, just adjust the shutter speeds so that the meter is physically lower (at f4, 2.8, etc).
Now if you want to stop the lens down, it can get complicated. The easy way would be to just set the lens to M and use stop-down metering **BTW the camera will still think your at f5.6**
The harder way would be to leave the lens in A mode. Set the aperture down N stops, but then adjust the shutter speed like you are going to over-expose by N stops. For example set the lens at F4 (2 stops down) and then set the shutter so the needle is 2 stops higher (at f11). -In other words, change the shutter speeds so the camera thinks you need to stop down your f5.6 lens to f11 (2 stops), then tell your lens to stop down 2 stops (in auto mode)
This sounds confusing and I have not tried it but I think it will work.