Bread – When you try to “catch” yeast from the air: is it normal for the flour and water to split

First off, it's good to understand the difference between active dry yeast and rapid rise yeast. Active dry yeast is a larger granule of yeast in which the outer shell is composed of mostly dead cells entombing the dormant nougaty goodness inside. It has to be proofed to seperate out all the cells and rehydrate the interior active cells.

Rapid rise yeast is a typically a combination of 2 different strains of yeast (so those with a very discerning palate might be able to tell the difference, I've never really tried). The granules of yeast are smaller and dried slower to preserve more yeast cells. Ascorbic acid is also added to push the yeast into overdrive a little faster.

A great video that helped me a lot is http://how2heroes.com/videos/dessert-and-baked-goods/yeast-101 I have noticed before issues with Rapid Rise yeast not proofing very well the second time around. Apparently it's designed to give you one really good proof and then die out (play hard and die young). Instant yeast however is Rapid Rise yeast without the hardcore party attitude. It's what they use at the King Arthur bakery test kitchen, so that's good enough for me! They say to use them interchangeably, but many other sites I see show a difference of about 20%.

2 Tbsp Active Dry yeast ≈ 1.6 Tbsp Instant Yeast

If you've truly gone anaerobic and the smell is off, you are growing things other than the intended cultures...

As a rule, I simply feed mine flour and water. No sugar. The cultures can get along fine with the flour. (I did read in a reputable baking book about adding leftover water from boiling potatoes, for the starches, but I haven't had a chance to try.)

If the smell is off, I would dump and start over in a more breathable container. Your entire goal is to grow the sourdough cultures and let them flourish in their happy environment. And as you've smelled, there is a distinctive scent of happy sourdough. Now if the smell has changed, you lost your scented sourdough and are now growing something else.

I've kept sourdough for over a decade, and it's from a culture that is 84 years old. But if it smells funny (or gets brightly colored mold), he's going down the sink faster than dishwater. It's just the nature of the beast.