Electrical – Two DC DC converter with different output – In series or parallel

Well, unless some kind of charge-balancer is used, most types of energy storage devices in series (batteries, capacitors, etc.) will charge unevenly. Since a supercap may be rated +/- 10% in capacity, imagine what happens when strung together and charged in series: the one with the -10% capacitance charges first, and the voltage across it goes higher than the others. Most supercaps are pretty picky about maximum voltage, and violating this will shorten their life. Now charge equalization can be done on a series set, such as KA7OEI's blog. They discuss a lithium-iron-phosphate pack that wasn't charging correctly and how they "fixed" it by utilizing a crowbar circuit for each cell. Any number of variants could be employed here. So it doesn't matter much what number are placed in series - any in series is taking a risk.

As for the best type of converter, in general, one DC-DC converter is always going to be better than two, since there are always more losses with more components. So if possible, buck or boost are generally more efficient than SEPIC or other combinational converters simply because there is one of them.

Using the capacitors in parallel with a boost converter would solve the issue of equalization and not require any charge balancing, so seems the simpler route. At first glance.

Note that 12v * 0.75A = 9W of output power. Assuming 90% boost efficiency, current draw from the supercaps would be a minimum of (9W + 10% = 9.9W so say 10W), P=EI, 10W=2.7v*I, I=10W/2.7v, I=3.7A. Some supercaps cannot supply much current at all, or do so with little efficiency and much loss. So make sure the caps chosen can handle much more than this current. When the caps discharge, their voltage drops... so Ohm's law dictates that to get 9W out of the boost regulator at 10% capacitor voltage (0.27v), 10W=0.27v/I, I=10W/0.27v, I=37A! That is going to require some good boost circuit design. Also, whatever is used to charge the caps, must be regulated to never go above 2.7v.

Now 600F sounds like a lot of capacitance and it is... but in terms of bulk energy density the supercaps may leave you disappointed. If constructed, you may eventually decide that a 12v lead-acid battery would last longer and cost far less. The self-discharge rate of such caps is fairly high, so they will not hold energy for years or even months. Of course if this is for a backup battery scenario that is normally powered and charging, then it would be more reasonable.

As one of the comments pointed out it is possible and desirable to use different MOSFETs for some sync buck converters. Often the duty cycle is low because you're converting from (e.g.) 12V to some much lower voltage like 1.2V. In that case the duty cycle is 10% (Vout/Vin) and the bottom FET is on 90% of the time. For that reason you would select a low RDSon device for the bottom FET. The top FET is only on 10% of the time, but is responsible for most of the switching losses. (The inductor current usually commutates the switch node to just below ground before the bottom FET turns on, making it a ZVS transition.) So what's important for the top FET is low gate charge and fast switching. RDSon can be much higher than the bottom FET because it's conducting only 10% of the time. As the duty cycle changes, these compromises will change accordingly.

There's a method for optimizing these choices called the J/K method (nothing to do with flip-flops.) You can see it here:

The J/K Method For FET Selection