RE: -----cub-----
Your batteries will be fine. Running your motor wide open while the plane is stationarly can lead to over heating if you do it too much. The motor will not get enough cooling air and your amp draw will be higher than it would be in the air.
If you want to drain the packs, do it at 1/4 throttle, but there is no real need to do that. Just flying the plane will be fine.
I usually recommend that you do the first charge or two at 1/2C. For a 1000 mah pack that would be 500 mah. Then at 1C, then up to 1.5C. This helps to form the pack more gently. Not mandatory but it has served me well.
You can buy all kinds of things btt they are not specifically for that plane.
Larger wheels would be good if you are taking off from grass.
8 cell pack will give you more power with a little less endurance, maybe.
There are X port options for the plane, from HobbyZone and ParkZone
Since that is a 27 MHz system, in order to do any mods to the electroncis or the motor you will need to gut the plane and start over, but there is really no reason to do that. It has plenty of power, especially if you pu in the 8 cell pack.
BTW, there are dozens of Super Cubs from many makers, so you need to be specific that this is a HobbyZone Super Cub RTF or people will give you advice that does not match your plane.