I know this has already been answered but my opinions are as follows:
1 - The best storage charge for your batteries is ~40-65%. You want to store them in an intermediate state. Definitely not full or extremely low. When I say "store" I mean if you are not intending to fly for a week or more. If you are going to fly within a few days just charge them full & you should be fine. If they are going to set for a week or more then 40-65%.
Phantom 3 batteries have a self-discharge feature. The default is 10 days so, after 10 days of sitting, your batteries will auto-discharge down to ~65%. You can modify this setting from within the Go app.
Note the setting is retained within the battery so you must set EACH battery individually. I currently have mine set to 5 days. Note that the discharge timer resets when you press the power button & there is no visual indication that the batteries are in the auto-discharge state. The latter is somewhat annoying & I think DJI should make the power light blink as a visual indication that an auto-discharge is in progress. The LED power draw would also aid in the discharge process.
I always charge my packs before I intend to fly. If batteries are >80% you can force them to top off by powering the battery on BEFORE attaching to the charger. With the auto-discharge feature this is a good idea.
2 - DJI recommends every 20 cycles discharging the batteries down to 8%. This aids in balancing the cells & calculating available power. I usually do this by flying & then hovering nearby until the battery drops to <8%. If your auto-land is set to the minimum of 10%, you will have to hold her in the air with the throttle manually for the last 2-3% or she will auto-land. Alternatively you can let her sit on the ground idling until the battery drops under 8%. I do not like leaving the Phantom on without props as a discharge method as it takes a lot longer to discharge & there is no air flowing over the electronics.
*Note that "cycles" calculated by the app may not exactly match the number of times you have actually charged a battery. It only seems to count a charge if the battery accepts a certain amount of charge. Several top-off charges may equate to only one actual charge cycle.
3 - Li-pos in general break in over the first 5-10 cycles before reaching maximum performance. From then on they are slowly degrading. Some folks live by a
"50% break-in rule" but I've never seen this as a DJI recommendation. When any battery is brand new you want to go a bit easy since it could be a dud. You certainly don't want to send your bird out 4 miles on a brand new untested battery!
Related some folks recommend landing @ 3.4-3.6 volts-per-cell. If you are going for the maximum battery life that may
(or may not) be good advice. I tend to push my batteries a lot harder & you CAN fly to 10% or even lower in a pinch, as long as you understand you have to force her to stay airborne by applying throttle once you reach 10%. I don't recommend doing this each & every flight but, on occasion, I doubt it causes any harm.
The critical voltage to remember is 3.0 volts-per-cell. 3.0 volts is empty. If any cell drops below 3 volts the battery shuts down. In the battery screen be sure to enable the option to show voltage on app screen. That way you see the battery percentage as well as the voltage of the lowest cell.
If you are way out, heed your flight controller's battery advice if it indicates a low-battery RTH! I recommend long-range mission begin INTO THE WIND so you have a nice battery cushion with the wind at your back on the way back home.
4 - I ALWAYS fly with a freshly-charged full pack. If your batteries are down to 50% & you are just going to touch down for a moment & take back off that is no biggie as the battery is still warm. I do NOT recommend using a partially discharged pack if you are going to come back later & initiate a new flight on a now-cold pack. Not to say you can't do it in a pinch if you closely monitor the voltage & limit your power demands but, as a new pilot flying an expensive aircraft, you have enough on your plate already without worrying about a mid-air catastrophic battery shutdown. Fly with a full-battery & you'll be good.