Guilherme,
I'm trying to figure out that same thing at the moment. Well almost. I did plan on having a aux alternator. Do a search of VAF and you will find most of what you want. If you don't want a second alternator like I do it is simpler. You can look at the Z-14 aeroelectric page that has 2 batts and 2 alternators as a start. There are also some references that show you how to use a couple of diodes to do the isolation.
I was trying to figure out my panel layout and then I realized I needed to figure out more of my electrical system before I could finish the panel.
Basically the idea is to have a separte Aux Batt power switch to enable your startup instruments. The Aux Batt bus can be powered by the Main bus through a high current diode. Th Aux Batt is then charged by the Main bus through a diode and series resistor for current limiting. Once the Main power switch is turned on it should then supply the devices instead of the Aux battery. There are lots of variations on this scheme so I'm trying to figure out exactly what I want. I couldn't find a schematic that has everything that I want so I think I'll have to start drawing my own.