Welcome, we've been expecting you. Everything you have read about your kit is pretty much wrong.
You've come to the right place for brewing knowledge. We are committed (yeah we should really be committed
) to helping you make great beer, and to getting the most out of this great hobby.
The second container is a "secondary" in the old days your moved your beer to that vessel after only a few days. But we have progressed in brewing knowhow, and we don't rush our beers out of the primary.
You will find that many of us leave our beers in primary for 3-4 weeks (or more) and only secondary if we are adding fruit or oak, or to dry hop (though many of us dry hop in primary now as well)....and we have found our beer vastly improved by letting the beer stay in contact with the yeast.
There's been a big shift in brewing consciousness in the last few years where many of us believe that yeast is a good thing, and besides just fermenting the beer, that they are fastidious creatures who go back and clean up any by products created by themselves during fermentation, which may lead to off flavors.
Rather than the yeast being the cause of off flavors, it is now looked at by many of us, that they will if left alone actually remove those off flavors, and make for clearer and cleaner tasting beers.
Even John Palmer talks about this in How To Brew;
Your beer will thank you by waiting.
Welcome to the greatest hobby there is! But just realize that you areno t making koolaid here. To make the best freakin beer possible, ignore what the recipe instructions saym and slow everything down..Your beer will thank you!