two 3 farad caps

Put the caps anywhere you want to in the circuit.  The safety factor comes into play when you are charging them with a slow trickle charge per directions.  If they are to perform at their best potential, they will be placed directly before the subwoofer amps.  The main power wire feeds positive and they may be grounded to chassis separately.  Distro blocks tame the install...they make things neater and more organized in appearance.  There is no additional safety factor when using those.

Without using a distro block, you can just as well solder wires together:

If there is only one sub amplifier, place the two caps in parallel before the amp.

Yes, they need to be wired parallel.  Parallel is simply wiring same polarity to same polarity.  Positive to positive, ground to ground (or chassis, which is common ground).  A cap can go before or after the distro block, it doesn't matter.  It all depends on what is involved in your setup and how everything fits in the car.  If I had one distro, two caps and two sub amplifiers, I would put the distro first...then wire from the distro out to each amp.  Just before each amp I would put a capacitor.

But if I had one cap, one distro and two sub amps, I would first put the cap, then the distro, then wire out to each amp.  I would also keep them all close together as possible.

Like I said, you can place the caps anywhere you want to in the circuit.  All pos to pos connections are parallel and thus instantly connected, whether through a distro block or not.  In your case, with one sub amp and two inputs into the distro...you are using only one input for the main power wire.  You can use the second input to connect one (or both) of the caps just to use all the connectors. 

Here is a way, putting one cap in parallel on the main power wire, the second cap uses the second input connector.  All ground wires go to chassis, or they can be collected together at a distro point and then to ground.  Grounding is largely experimental.

It doesn't matter where the caps are located.  The amp that wants to pull from them will do so, even if the caps are on an (distro's) output wire in front of one of the smaller stereo amps.   Arrange your installation however it fits best and looks the neatest, keeping wires short as possible.