After the battle on day 1, you get an item. It will be displayed in green text above your upgrade options. You can check what it does in Info -> Items. On day 1 of loop 1, you can change it there to any of the 8 starting items.
Some things mentioned in what I wrote that may or may not have been immediately clear:
5EE Commander = The Mentioned 2 Capture 4 Surround Commander.
Chosen Vulnerabilities are classified in Minor, Significant and Core for the 4 circumstance types, Hate/Pleas/Inj/Dig
All Vulnerabilities will be spread over all chosen so that there is exactly 1 Core weakness for each of those 4 types, with all chosen having at least 1 core weakness, and 1 having 2.
The same goes for all other types of Vulnerabilities.
Each of these vulnerabilities can be broken 4 times, as seen in the profile of the chosen.
1. You need to deal enough circumstance damage that the chosen would reach 10K in that circumstance. Using an Action (Which gets highlighted in green) will then cause the Tier 1 break. Note that you can use surround actions that do not actually affect the vulnerability you want to break. (Check profile, they will be listed.)
2. You need to reach 10K circumstance damage and use the new yellow marked attack option while the chosen is surrounded. Using that action causes a Tier 2 Break.
3. Tier 3 Breaks happen by themselves, and explain themselves when they become available in the chosen profile. For them to happen, you need to reach high enough accumulated trauma damage. That's what the Orgy is for, as it otherwise is nigh impossible to get the required Trauma values in a timely fashion.
4. Tier 4 Breaks are also rather self explanatory. Check the chosen profile after tier 3 break.
Each break makes inflicting trauma and circumstance damage for that type on that chosen easier.
The relationship between chosen is determined by the order of breaking Core and Minor Vulnerabilities of a type (For example, the relationship between your core morality and your minor morality vulnerability chosen is determined by those). (Significant don't matter). I Personally recommend breaking core vulnerabilities always first, it is the simpler and usually safer option later.
Beyond step 7 the game becomes self explanatory, IMO. My big hangup starting the game was getting past that point. And well, understanding the need of the 5EE Commander.
And again, grab Networked consciousness (the upgrade) as soon as you can. It is really, really good. I usually start the mad dash for it after my first 5EE Commander deployment.