Afternoon Mark
There's a comprehensive guide to flashing here ...
http://www.fixmyroof.co.uk/install-roof-flashings/
If you want to nail your soakers to the laths, I think you'll have to get the slates off. It can be done without breaking them if you're careful and cover the slate with something (hardboard?) before you lever against it to pull out the nail. Alternatively, since you did it properly and used copper nails, you can get a slate ripper up to cut them .
Don't forget the patination oil.
Cheers
Dave