Well you need to plan out the migration first.
How many computers you have on each site? if 200 or less at each site then
On your main site you have already installed the SEP Manager Console ( I beleive) --FOrget about Disc 2 you wont need that
You have to make 5 groups in SEP Manager one group in each site..well you can have sub-group as well if need to drill down further.
Now start deploying the SEP client on all your computers inclucing the Secondary servers.
Then Make all your secondary servers as Group Update Provider (GUP)
These GUPs will act as secondary servers as you had in SAV.
Please read this doc for more information on GUP
Symantec Endpoint Protection 11.0 Group Update Provider (GUP)
http://service1.symantec.com/support/ent-security.nsf/854fa02b4f5013678825731a007d06af/184f7ebb04cd173480257363006d2beb?OpenDocument