OK, still can't quite wrap your head around(
grok) how it works? it's no problem. Unless you have done some real programing, or electrical engineering it can be hard to see how it works. Lets slow it down a little.
The Node order in the AkAbak wizards is s=t=u=v(=w=x) for reference, if you need it. Moving on...
Lets talk about the original sealed enclose, and it's dependency tree again.
A sealed sub is made up of a driver, an enclosure, and it needs a signal source to make noise. This can be represented as two different systems. An electrical , and a physical.
On the electrical side you will need two path connections.
Commonly called positive(+) and the other negative(-), or Red and Black by some.

In AkAbak these connection points are called Nodes. As +/- power tabs are a universal need, AkAbak has set Node=0 for negative, and Node=1 for positive by default. We can map that out as:
1- Voltage -0 This represents the voltage supply, and it has two Nodes, 0 & 1. In AkAbak Nodes are assumed to be following a path from left to right, so the Positive will flow to the Negative. You get 1- to -0 this way. This is also true for the physical components as well.
The physical side consists of the driver and enclosure. On the physical side only the path of the sound waves matter. A driver can emit sound from both sides of it's cone, so it would have two physical nodes. A sealed enclosure only has one spot where waves can enter and leave, so it will only get one Node. We could draw it out as:
Enclosure -? and ?- Driver -?
I use question marks here as it is up to you to choose the numbers of the nodes. The only ones that are assigned are 0 & 1. Lets make the driver use Nodes 100 and 120:
100- Driver -120 or
120- Driver -100
Either way is fine. Now we need to attach the driver to the Enclosure. As it only has one Node all you have to do is decide which node you want to attach it too 100 or 120. As mentioned earlier the flow is from right to left. In this way (in-phase)sound flows from the the driver to the right. With this in mind the enclosure should go on the left:
Enclosure -100- Driver -120 or
Enclosure -120- Driver -100
Let's go with the first option, to help keep the right to left flow going in our numbering as well.
Now you have to connect the waves with the air outside the enclosure. You need to add a Radiator to do this. As the drivers forward facing cone is the only thing "
pushing any air" the Radiator need to be the same size as the cone, and attached to the front side. A Radiator only has one Node connection, so it gets attached to 120. The same spot as the front of the driver.
Enclosure -100- Driver -120- RadiatorYou don't have to worry about figuring up how many Nodes a component has. When you go to install one there will only be one Node box to input anything. 
A Driver contains an electrical side as well as a physical, and needs a voltage in and out to function. In AkAbak the electrical side comes before the physical, so when looking at a Drivers Node indicator it looks like this
E=E=P=P. We have
E=E=100=120 now. To connect the driver in the correct polarity it needs to flow from the first E to the second. This gives us
1=0=100=120. If we wanted to reverse the polarity we would switch the 1 and 0 around at the driver.
This can be mapped out as:
1 voltage 0
Enclosure 100 Driver 120 Radiator
On paper I would have drawn lines to the Nodes connecting the electrical and physical rows, but I used colors here.
The finished code in the Linking section should be Noded like this:
Driver 'D1' Def='Dayton RSS390HF-4'
Node=1=0=100=120
Enclosure 'E1'
Node=100
Vb=315L
Lb=1m
Radiator 'Rad1' Def='D1'
Node=120 x=0 y=0 z=0
HAngle=0 VAngle=0
There is no limit to the amount of components connected to a single Node point. If I wanted to add another driver in paralel to the enclosure I could just add another Driver and Radiator Link, and connect the rear of the driver to the same Node 100. The forward side of the driver would need to be assigned a new Node to attach a new Radiator for it.
Driver 'D1' Def='Dayton RSS390HF-4'
Node=1=0=100=120
Driver 'D2' Def='Dayton RSS390HF-4'
Node=1=0=100=121
Enclosure 'E1'
Node=100
Vb=315L
Lb=1m
Radiator 'Rad1' Def='D1'
Node=120 x=0 y=0 z=0
HAngle=0 VAngle=0
Radiator 'Rad2' Def='D2'
Node=121 x=0 y=0 z=0
HAngle=0 VAngle=0
If you wanted to attach the new driver in series you would need a new Node to join them. Power would flow into D1 from Node 1, then it would not go back to Node 0 you need it to travel to the other Driver first, so we name the first electrical Node on D2 as 2. Now power can flow from 1 through D1 to Node 2, and then through D2 back to 0.
Driver 'D1' Def='Dayton RSS390HF-4'
Node=1=2=100=120
Driver 'D2' Def='Dayton RSS390HF-4'
Node=2=0=100=121
Always remember to make sure you keep everything flowing in the same direction. If you switch anything around it will reverse the polarity of the Driver, and cancel out the sound from the other Driver.
