If I was attempting that system with those freqs, I would have the sites/campus separated and my freqs file would more look like this. Notice the 99 ?  Thats your starting point as seen below in the dsdplus notes. I always followed notes and populated with 99 but as 
@cg posted, looks like you could use a ?  also.
Since site 2 freq 453.6250 is being shown as channel 1 & 2, that's the 1st cap+ repeater.  Easiest way is to park on each freq until it spits out which cap+ repeater it is.
Georgia site 1
Cap+, 7, 1, 99, 461.612500, 0.0, 0
Cap+, 7, 1, 99, 463.250000, 0.0, 0
Cap+, 7, 1, 99, 464.925000, 0.0, 0
Georgia site 2
Cap+, 7, 2, 1, 453.625000, 0.0, 0       1st cap+ repeater ch 1 & 2
Cap+, 7, 2, 99, 453.862500, 0.0, 0
Cap+, 7, 2, 99, 453.387500, 0.0, 0
Cap+, 7, 2, 99, 460.262500, 0.0, 0
Cap+, 7, 2, 99, 453.487500, 0.0, 0
Georgia site 3
Cap+, 7, 3, 99, 453.312500, 0.0, 0
Cap+, 7, 3, 99, 453.037500, 0.0, 0
Cap+, 7, 3, 99, 453.137500, 0.0, 0
Much easier to determine lcn on one site at a time. I also never attempted to do more than 1 site at time.
Dsdplus notes
  Cap+ monitoring
  ---------------
    Follow these steps to monitor / follow the rest channel and voice calls on a Cap+ system
     a) select a network ID
        Cap+ systems do not broadcast a network ID
        If the system has been added to the RadioReference database, use its page number
        Otherwise, assign the system a unique NID (9999, for example)
     b) create an entry in the DSDPlus.networks file
        Example:
          Cap+, 9999, "Mayberry PD"
     c) if the network has multiple sites, create entries in the DSDPlus.sites file
        Example:
          Cap+, 9999, 1, "North"
          Cap+, 9999, 2, "South"
          Cap+, 9999, 3, "East"
d) for each known system frequency, create a channel record in the DSDPlus.frequencies file
        Initially, use invalid channel numbers
        Example:
          ; Mayberry PD North
          Cap+, 9999, 1, 99, 450.5000, 0.0, 0
          Cap+, 9999, 1, 99, 451.2625, 0.0, 0
          Cap+, 9999, 1, 99, 454.9125, 0.0, 0
          Cap+, 9999, 1, 99, 455.5000, 0.0, 0
     e) tune CC FMPA/FMP24 to an active system channel (note: TCP link required)
        CC DSD+ will scan the DSDPlus.frequencies file for a Cap+ record with the same frequency;
        The first matching record will be used
        CC DSD+ will use the frequency record to establish the system's network ID
        CC DSD+ will use the NID to display the network and current site names
     f) at some point, DSD+ should determine the channel's ordering
        and display it in the event log window
        Example:
          "450.500000 is first Cap+ repeater (Ch1 and Ch2)"
        Use the information to edit the channel's record in the DSDPlus.frequencies file
        Note: continue to use invalid channel numbers
        Example:
          Cap+, 9999, 1, 101, 450.5000, 0.0, 0
     g) repeat e) and f) for each active system channel
        Example:
          "451.262500 is third Cap+ repeater (Ch5 and Ch6)"
          "454.912500 is fourth Cap+ repeater (Ch7 and Ch8)"
          "455.500000 is second Cap+ repeater (Ch3 and Ch4)"
          Cap+, 9999, 1, 101, 450.5000, 0.0, 0
          Cap+, 9999, 1, 105, 451.2625, 0.0, 0
          Cap+, 9999, 1, 107, 454.9125, 0.0, 0
          Cap+, 9999, 1, 103, 455.5000, 0.0, 0
     h) when the ordering of all of a site's active channels has been determined,
        edit the channel records so they have the correct channel numbers
        Example:
          Cap+, 9999, 1, 1, 450.5000, 0.0, 0
          Cap+, 9999, 1, 3, 455.5000, 0.0, 0
          Cap+, 9999, 1, 5, 451.2625, 0.0, 0
          Cap+, 9999, 1, 7, 454.9125, 0.0, 0
        CC DSD+ will now automatically direct CC FMPA/FMP24 to follow the rest channel
        and direct VC FMPA/FMP24 to follow voice calls