updating to el c and replacing drive

[joec]

i have updated snow leopard to Capitan on an external drive and still have a clone of the snow leopard. The internal drive has been dead for awhile and i am having it replaced. Capitan will be installed on the new internal drive by the repair guy. i intend to restore to the new drive the Capitan upgrade i already have because of a firewall program that survived the upgrade but can't be installed cleanly because of the new security protections. i understand that i need to download a SD update from your website. my question:

will those security protections prevent a smart update?
if i do a clean restore, should i wipe the internal disk using SD or would it be better to boot from the snow leopard clone and use disk utility to reformat?