1) Do I just add up all of my proceeds and subtract all of my basis?
Yes. Although you ought to be using FIFO, so using the basis of the earliest coins you owned.
2) Let's say you have an account with 10 BTC you've held for over a year. You then purchase 1 BTC at $400 and sell it an hour later for $401. Do you have short term gain of $1 or long term gain of $1? Is there a way to keep your long term holdings separate in order to day trade while still keeping a long term position in order to take advantage of the lower rate.
The default is FIFO, so you would have long-term gains of $401-$x from your 10 BTC pool. You could use LIFO (last-in-first-out) but you should use it consistency and not to avoid taxes. The IRS might not accept it in an audit.
If you maintain separate wallets and separate exchange accounts, then you can keep one for investment and one for spending. As long as they never mix.
3) Break even transactions: If I buy 1 BTC at $400 and sell it a month later for $400, $400.01 or something else that rounds to $400, does it have to be reported?
All capital gains transactions have to be reported. However, they round to nearest dollar (so $0) on your tax forms.
and anyway every amount that do not surpass $600 per year, is not taxable
This is wrong. There are no limits for capital gains in the US, everything is reportable. You are confusing the 1099-MISC business form requirement.
See
https://bitcoin.tax for more information and to help calculate your capital gains and income.