Because of identical LCN's; you MUST program each site as separate systems. In your senario, you would then have to enter each talk group for each site. However, I would limit the talk groups to the sites with their intended primary coverage (if that makes sense). For example, in the Lynchburg area system, I only enter the Lynchburg groups for the Lynchburg site, the Amherst County groups on those 2 sites, and the Bedford county talkgroups on those 2 sites. No wildcards for any site. Whether you place all in one scan list or divide by locality is up to you. Personally, I do the latter.
For Spotsylvania, I duplicate everything there. For the commercial system in Pennsylvania, If you're going to be in range of more than one site, you'd need to duplicate as needed.