Can't apply transitions to After Effects comps in Premiere Pro

Hi people, newbie Premiere user here (my boss is trying to convert me from FCS) :-)  I downloaded the trial version of CS5 and want to learn as much as I can before my initial 30 days is up.  My initial experience has been pleasant, but I've come up against an obsticle I could sure use some help with.
1)     Creating my timeline with serveral clips
2)     Exporting certain clips to After Effects; 'Replace with After Effects composition'
3)     Adding my effects
4)     Back in Premiere Pro my clip is replaced by the comp.
5)     Try to apply a simple cross-dissolve across 'Comp 01/Comp 02'
PROBLEM!
Seems the transition will only snap to the start of the second comp.  With clips I can drag & drop the effect to span the clips and get perfect results, but not on an After Effects comp.
6)     In Premiere Pro 'Effect controls' change parameter so that the transition centre is at 'cut'
The result indeed spans the clips, but the effect quality is terrible - decent fade from comp 01 to a sudden dip to black before fade-up on comp 02.
Yes, I understand the 'Layers' concept, but I'm not asking the software to do anything nonsensical, just a simple cross-fade across 2 comps.
I really would appreciate any advice anyone can offer, I'd really like to be converted (mainly because if I AM my boss has promised to buy me a licence when my 30 days are up!) :-)
All the best
Steve

To expand a bit on Colin's comments, back in the film days, the concept of Handles was easy to grasp, as the pieces of film were on an A and a B Roll, and the editor had to physically overlap them by the desired amount, so that the lab could print with a Dissolve. The same held for the days of A-B Roll digital editing, where the Clips were again physically overlapped on separate Tracks. Then, digital editors were developed that allowed one to edit with the Clips on a single Track, and where Transitions were applied between them. The Handles were necessary still, but were no longer visually obvious.
These images will tell you a bit more about the concept:
Hope that this helps,
Hunt

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