NMOS High frequency, fast bi-directional switching, 12V 100A
1)  You can face the body diodes either way and it will work, but I usually have the source terminal of both MOSFETs connected together.  That way your gate-source driver is only between two points rather than 3.  For NMOS this would mean the diodes point away from each-other.

2)  To turn on the MOSFET you only need to develop a voltage between the gate and source.  You don't need any sustained current to flow through the source.  Some small amount of current will flow between gate and source when the gate is initially driven as the gate capacitance charges.

2/3)  If you use a proper gate driver with the sources tied together you won't have to worry about the gates floating because the driver will always determine the gate source voltage.  One way to drive NMOS FETs is with an isolated supply that was made for gate driving, combined with a gate driver chip.

For example you could use this floating power supply...

MGJ6D121505LMC-R7

Vin = 9V to 18V.  Dual isolated output voltages +15V and -5V with shared floating ground.  Available on Digikey for $16.75.

http://www.digikey.com/product-detail/en/murata-power-solutions-inc/MGJ6D121505LMC-R7/811-3235-1-ND/6202209

With this gate driver chip

1EDI60N12AFXUMA1

Available for $2.87 on Digikey.

http://www.digikey.com/product-detail/en/infineon-technologies/1EDI60N12AFXUMA1/1EDI60N12AFXUMA1CT-ND/5962298

When using MOSFETs in parallel you have to worry about the fact that they don't all switch on at exactly the same time.  So one of them always takes a lot of current for a short period just following a switch, which stresses it and leads to early failure.  Also they will share current, but it won't be 100% equal so some will get hotter than others.  You might have an easier time just using one MOSFET that is rated for 100A.  For example you could use this one...

IXTN660N04T4

It is available for $19.60 on Digikey.

http://www.digikey.com/product-detail/en/ixys/IXTN660N04T4/IXTN660N04T4-ND/6053919


It is rated at 660A continuous current provided that you can cool it. It has a 0.85 milli-ohm on resistance. So at 100A the drop across it would be 85mV and 8.5W of heat would be generated.

The device has a large isolated pad on the back side that has a junction to pad thermal resistance rated at 0.144 C/W. The pad has screw holes for mounting. So you could theoretically put that isolated pad right on the frame of the vehicle to sink out as much heat as you need.


IXYS corporation sells other similar MOSFETs if you need a different package style.


I see you have a 1 ohm resistor as over voltage protection for your alternator.  If your alternator can really put out 100A then you probably need a much bigger resistor.