Electronic – Synchronous DC-DC converter and fast diodes

using a Schottky diode in parallel with the low side MOSFET will prevent the body diode from conducting

Will it really? I see this a lot, and a naïve analysis would suggest so. After all, the forward voltage of a Schottky is less than that of the silicon PN junction of the body diode, so how could the body diode ever become forward-biased if the Schottky is forward-biased first?

But this neglects that real circuits have inductance. Really what you have is this:

^{simulate this circuit – Schematic created using CircuitLab}

(CircuitLab doesn't seem to have the appropriate Schottky symbol)

Now say we set \$V_{GS} = 0V\$. The current \$I_{DS}\$ that was flowing in the channel now must find another path. It can go through the body diode, D1, or through the Schottky, D2. The path through D1 has a very small inductance, because the current path need move some microscopic distance. However, D2 is maybe some millimeters away, which has, even with the smallest SMT parts, many orders of magnitude more inductance.

Thus, at least for some brief period after the MOSFET channel closes, current will go through the body diode. The additional inductance (L2) puts a limit on how fast current through D2 can rise, and since the voltage across L2 is clamped to the forward voltage of D1, less the forward voltage of D2, current can't rise all that fast.

Sure, L2 isn't all that big, and you don't have to wait that long. But the whole point of this synchronous rectification is to avoid conducting through either of these diodes at all, so naturally you are going to make this time as short as you possibly can. In light of this, does adding D2 really do anything?

Is there a procedure to find a small yet safe dead time for the complementary PWMs?

I don't think there's any magic method. Measure accurately with a scope, and read datasheets carefully. Depending on what sort of gate driver you are using, maybe there are things you can do to make the gate switching delay smaller and more predictable. For example, if there are common-emitter BJTs in your gate driver, then you can use a Baker clamp. It's also common to design gate drivers to sink more current than they can source, so that turn-off is faster than turn-on. Or, you can measure the storage delay accurately, and compensate in software.

You can also do things to limit the shoot-through current, including a resistance or small inductance in the path, for example. However, this works only to a point, since by introducing such a thing you are also introducing an additional loss.

If the gate is tied low, then the mosfet won't turn on (like the two lower mosfets in your circuit) It will then function like a really high value resistor, and would be pretty pointless to use a mosfet like this in a circuit. Modern mosfets also have reverse current protection with a body diode (some have this left out)

EDIT: Additional question, one more question is that if you look at the MOSFET on the primary side it has a diode connected parallel to it(i was told that this is the body diode and not an external diode), but on the secondary side the ideal NMOS doesnt have the body diode shown. Why is that?

You need to check the mosfet spice model to see if it has a built in diode into the model. In spice it is all up to you to know what your modeling, if you really wanted to you could put in any circuit file tied to what looks like a mosfet.