Additions:
Pro: Simple to manage just one account.
Con: Can not separate report (click-through / impression) for multiple account
Con: Can not select different set of merchant sets.
Con: Can not set different SubID for each site.
Con: Can not set different Affiliate Site IDs for each site.
===2. Use Multiple DFF Accounts===
Pro: Capability to select different set of merchants per site.
Pro: Capability to set different set of default SubID per site.
Pro: Capability to set different Affiliate Site IDs per site.
Pro: Capability to see reports click-through & impressions per site.
Con: Require different email address for each DFF account.
Con: Need to remember multiple DFF account logins.