Double the barm???

Although I'm only familiar with Reinhart's Bread Baker's Apprentice and not his other books, I do know that the quantities of starter (a.k.a."barm") he indicates building and keeping in BBA is a tad excessive. 

I can understand if one were baking every day and/or in very large quantities where a few cups of starter may be useful since you'd use most of it up regularly. But as the majority of people are more likely to be weekend bakers, this is, IMVHO, excessive. Since feeding and refreshing a few cups is going to get expensive and wasteful, not to mention storing taking up fridge real estate, it's just as easy to keep a small quantity as your Mother starter and increase this to whatever amount you need for any particular recipe in one or too refresh feeds prior to making your bread of choice.

Myself, I keep 50 grams (about 1/4 cup) of Mother starter and this is made up of a 1:2:2 ratio from 10 grams starter and 20 grams each flour and water. Feeding then gives me 40 grams of excess (a.k.a 'discard') from which I can in one feed, get 200 grams or in two feeds, could get up to 1000 grams, if I needed, all by keeping to that 1:2:2 feed ratio.

Of course, if I need, say, 340g, I can take that same 40g excess and give it 150g each flour and water and I'll have 340 grams in a little longer than the time it might take to inoculate 200g. Or two feeds adding 75 grams water and flour each time. The actual amounts are flexible and depend on your recipe's needs. 

Bottom line, however, is you don't need to keep and feed a few cups of starter in a 2 quart jug. A pint or even half pint jar can do you just fine if you keep 50g of Mother.

The above is only what I do; others keep a little more and some keep even a little less. You can decide how much makes sense for your baking needs. But I'll bet 3+ cups is way more to what you'll ever use.

As to the parchment question:

I am not personally aware of any reason why parchment would cause the bottom to bake darker. You don't indicate if you're using a stone or baking pan which may need handling slightly differently. Also, we don't know how well your oven is heating, if there are hot spots or if the thermostat is accurate. These are things you should be keeping an eye on by using an oven thermometer to help double-check how your oven is working.

You'll likely find that the temp you set the oven at is not exactly what the oven actually reaches. Based on reading your oven thermometer vs accepting what the thermostat or digital display on your oven says, give the dial a few degrees up or down as necessary to reach your desired temp.

Oven thermometers can be had at most any kitchenware department for about $5 or so (here's a bunch from Amazon). They may not be the most accurate things in the world at that price point but they will certainly be helpful to indicate if your oven is too hot or too cool. 

So here's a way to keep your bread from being too dark on the bottom if you use a pan: Use two. Using similar baking pans, you can put one into the other and build a bit of an insulation layer. Or you can put an extra oven shelf below the shelf you bake on and slip a pan on there to deflect the direct heat from the element below. 

Likewise, if you're using a stone, putting the bread on parchment onto a pan and the pan on the stone will give you a little insulation from the heat. Although this may interfere with the point of baking on stone a little bit, the stone will still help regulate the oven temp and even with the pan give some fast heat to the loaf and get you oven spring.

UPDATE: Just saw your other post so now we know a few more things: You have a new oven stone and probably know about double-checking your oven temp already. Hope this is still helpful though.

Reinhart's instructions were a bit confusing to me as well but I think I've figured them out now.  My problem was that I hated to throw all that excess starter away, having been raised to abhor wasting food.  It is, however, a pretty small amount of stuff you;re dumping when you consider the cost per pound of flour.

I keep my starter in a 46 oz pickle jar with a lid that has a small hole drilled in it.  I place a piece of cotton over the mouth of the jar and screw the lid ont top of that to keep critters from getting in.  I have a second, identical, jar as well.  When I refresh my starter I place the empty jar on my scale, zero it out and then add 4 ounces of the starter.  The rest of the old starter gets thrown out.  I then add 2 oz of flour and 2 oz of bread flour to double the quantity, let it rise and when it's doubled, place it back in the fridge.  That means my starter, really it's a mother, is hydrated at 100%.

To prepare a starter for use in a sourdough formula, I check to see how much starter the forumula requires and then, divide the weight in half.  (For formulas that don't give weights I use Reinhart's standard of 7 oz per cup of 100% hydration starter.)  That number is the weight of mother I take out.  The other half quantity is split into 2 equal weights, one for the water and one for the flour.  I mix all that together and I get a 100% barm that is doubled from the mother.

The explanation of any process usually looks way more complicated than the actual process turns out to be.  This is the case here too.  A good scale, some simple math and you'll be cruising along with your wild yeast barm with ease.