Since no one replied I went and got it done myself. Took some searching.

Code:
on *:start: { 
  server network1 6667 -i Soul
  server -m network1 6667 -i Maka
  server -m network1 - i Soul
}

on *:connect:{
  if ($network == network1 && $cid == 1) { nick Soul } 
  elseif ($network == network1 && $cid != 1) { nick Maka } 
  elseif ($network == network2) { nick Soul } 
  else return
}

on *:NOTICE:*/msg NickServ IDENTIFY*:?: { 
  if ($nick == NickServ && $network == network1) { iden } 
  elseif ($nick == NickServ && $network == network2) { iden } 
  else return
}

raw 433:*:{ 
  if ($2 == Soul && $network == network1 && $cid == 1) { ghost Soul } 
  elseif ($2 == Maka && $network == network1 && $cid != 1) { ghost Maka } 
  elseif ($2 == Soul && $network == network2) { ghost Soul } 
  else return
}

on *:NOTICE:*has been ghosted.*:*:{
  if ($network == network1 && $cid == 1) { nick Soul } 
  if ($network == network1 && $cid != 1) { nick Maka } 
  if ($network == network2) { nick Soul } 
}

on *:NOTICE:*You are now identified for*:?: { 
  if ($nick == NickServ && $network == network1 && $cid == 1) { 
    join channels
  }
  elseif ($nick == NickServ && $network == network1 && $cid != 1) { 
    join channels
  }
  elseif ($nick == NickServ && $network == network2) { 
    join channels
  }
  else return
}