First of all what generator do you have 4500 watts?
I think from your post you have a two winding generator which means each winding produces 120VAC.
There is no reason not to use the Reliance switch as intended. You can run one winding to three circuits the other to the other three. As long as you are not combining the two windings you can use the full potential of the generator.
Trying to run one winding for your Reliance Transfer switch is the fast way to burn that winding out. It is NOT designed to run at 100% load and 80% load is a stretch so if you do this use the load meters to keep your winding below that. Given you now have a 2250watt generator max at 100% load you need to keep it below that around 75% to assure your generator will not melt the winding.
Also the PDF you mentioned is excellent.
You are planning to use a portable power device to power your residence. That means unless you removed the jumper in the generator panel or at the bell of the generator you have what is known as a "bonded neutral". NEC Article 250 will tell you that you need to remove the neutral to ground bond on the generator which is known as a "floating neutral".
http://www.mikeholt.com/mojonewsarchive/GB-HTML/HTML/NECArticle250Sections250.20-250.34~20020124.htm
All this really means and the PDF mentions it is that you carry the two windings (hot leads), neutral and ground through to the breaker panel in your house just using the Reliance box to pass those through. You connect the neutral to your neutral in the house panel box the ground from your generator is is grounded to the panel box itself. The power windings are connected to your 3 circuits per winding and those are connected to whatever breaker you plan to use (Reliance installation video is excellent in showing how to do a 6 circuit install).
For years it was acceptable to use a bonded neutral at the generator but the problem arises when the neutral between the generator and the residential breaker box is not connected. You then have a hot ground. Again this has been done for years but do yourself a favor and disconnect it and placard the generator as such "floating neutral".
To use it for portable power again all you need is the L14-30 male plug with the neutral and ground connected. That will return the generator to portable use "bonded neutral". Or you can use one of your duplex plugs and do the same thing.
I am confused as to why you would not use both 120 windings to power 6 circuits all staying at 120. The only way you get 240 is to tie two of the circuits from the Reliance box to a breaker that uses 240 like your AC, stove or electric dryer.
Use your VOM to check the continuity of the neutral and ground connection at the generator once you have disconnected the jumper be it at the generator panel or the bell of the generator. It will read 0 ohms or no resistance when connected and most likely OL or out of range when they are disconnected. That is what you want.
I am a EE by trade and have used Reliance boxes and interlock panels as well to provide emergency power and would be happy to help you get full use out of your generator.
Be advised that your insurance for the house can be voided if you don't do this right given it can be considered an unsafe condition.
Reliance makes some great equipment as do others like Generac. Why not use your generator (it was 4500 watts right?) to its full potential.
If you are not comfortable modifying the panel and doing this wiring get some help from a licensed electrician that knows how to wire portable generators for home power. This isn't something most electricians do often and be sure to ask them if they have experience. You might only pay a small amount for the minimum labor he or she would charge but it would be good peace of mind. Also not sure in your area if this has to be inspected by a local authority or not. Some locals do some don't.
Key feature of the Reliance system which I like over interlock panels is that you don't need to throw the main breaker killing external power and not knowing when the power comes back on. It allows you to leave a light on in the house so when utility does come back on you have an indication of that and can then shut your generator down once switching the Reliance panel back to utility feed...
Hope this helps some and happy to help you if you need it...