when i rewire z's, and I have done more than a dozen, i like to use plenty of relays as you are describing. I build a relay block and locate them all in one place, typically under the dash passenger side. Glove box would also work however you dont really need to get to them often when it's done correctly.
Typically I use headlight relays (2), horn(1), turn signal (2), fuel pump (1), ignition relay(1), optional brake light (1), optional starter (1), and for an efi car I include: coil pack relay (1), ecu relay (1), and injector relay (1). as I said , these can go out of sight, just well labeled and organized. The new fuse blocks you may want to have more accessible.
as far as lighting circuits, on a new fuse block you can get away with one 30 amp circuit for headlihgts. If you want to split into two circuits(l&r) you probably need to add an additional relay to the lighting design to control the individual light circuits together. maybe not though.
for the panel, I suggest that you keep it simple, clean and uncluttered. what ever layout you like, but less is more.