I tried to reassemble your payload how you explained it, but wasn't sure what the “multi port docking” thing was. If you are using the grey and yellow multi point connector that won't let you dock. Instead I put a clamp-o-ton docking port on the top of the payload. That way once we get one to orbit we can just launch a second one and dock them together.
Here is what I came up with:
You can also see the Mech Jeb vessel information in that screen shot, saying we are at 1.33. I try to keep my TWR around as close to 1 as possible when the stage begins. That is efficient but boring (since your craft moves sloooooowwwww). In my opinion anything around 1.15 is acceptable. In this case I would put more fuel in the payload stage but that doesn't really matter.
Also note that MechJeb tells us that that stage will last 96 seconds. I haven't really tested the accuracy of that number, but I use it as a guide line. It is important to keep that number in mind if your lifter stage isn't able to put you in a stable orbit. You have 96 seconds to make a stable orbit and boost yourself to your intended orbit.
Next up we need the lifter stage. The Payload and Orbit stages weigh 16.87 tons. A single mainsail engine can push about 150 tons and weighs 6 tons. That means we could simply put 1 mainsail engine and 127.13 tons of fuel on board. That would look something like this:
Also, all of that weight information I just gave was pulled from MechJeb.
We can see from the screen shot that a single main sail can push 7 of the X-200-32 tanks (half orange tanks), enough fuel to last for about 205 seconds. Again this probably isn't long enough to get us into orbit.
We have good TWR but not enough fuel. If we add more fuel our TWR will drop, so we will have to add fuel and engines.
If we stick with main sail engines, we can add 7 more fuel tanks for each one. For what ever reason, I generally go with 4, like so.
We essentially have a booster stage of 4 self contained stacks. Anyone of those mainsails can push all of the fuel above it and the center stack (our lifter stage) can push its fuel and our payload.
But the most important part of the design is here.
Each of the 4 external stacks feeds the center stack (our lifter stage). That means our lifter stage doesn't have to use any of its own fuel until the external stacks run out.
Here you can see what I mean.
I took this screen shot when our booster stage ran out of fuel and the lifter stage had to consume its own fuel. Our craft makes it to 32km before it has to shift over to lifter stage only.
I always consider all the speed and altitude of the booster stage to be “free,” since it is as if we were just dropped at this point going 958 m/s. Our lifter has all of its fuel.
For the record, the whole point of that ship was to make a clear example of the ideas of booster and lifter stages. The thing actually exploded seconds after that last screen shot. It is way too tall.
I hope that helps. If for some reason you are reluctant to get MechJeb you can always experiment. Build a payload and add fuel to the lifter stage until it has barely enough thrust to take off. That is your 1 to 1 point.
If you really really want to push the limits, get your TWR around .9 and then add solid rocket boosters. You'll burn of that .1 by the time the SRBs burn out... most of the time.