APR = Annual Percentage Rate and it's the interest paid for holding SBD. This APR is dynamic and it's set up by witnesses, you can see the number set by each witness on http://steemd.com/witnesses. In the early days of Steemit, when SBD wasn't gamed, holding SBD was subject to up to 10% interest (to incentivize people to hold on to it).

The savings account is a protection feature. If you want to put aside some funds, you should do it there. The 3 days withdraw waiting period is a safety guard, in case your account gets hacked. Basically, if somebody takes over your account, he will not be able to withdraw your savings immediately, giving you a 3 days time window to react (freeze your account, recover your keys, etc). That doesn't happen in the main STEEM account, where funds are always available.