Theres many ways to train. Such as simply going into the academy grounds and practicing your jutsu like so, reading and studying hand seals to increase intelligence, or even simply water walking to increase Chakra, the follow will help your training.

STR: Doing training such as pushups, situps, sprints and or anything that deals with physical Strength.
INT: Studying from books or determining peoples moves increases intellgience
DEX: Throwing projectiles such as kunai and shadow boxing
SPD: Sprinting, or anything that deals with fast movement...
Chakra: Goes up with Intelligence and Dex
Stamina: Goes up with STR and SPD

Missions help alot with stats increasing them by diffrent levels.

D Leveled Missions: Chakra/Stamina increased by 1 HP Increased by 1
C Leveled Missions: Chakra/Stamina increased by 2 hp increased by 2
B Leveled Missions: Chakra/Stamina increased by 3 hp increased by 4
A leveled Missions: Chakra/Stamina increased by 5 HP increased by 6
S leveled Missions: Chakra/Stamina increased by 10 HP: Increased by 15

Every few missions your able to increase your stats by one.

4 D leveled missions = 1 Free Stat
3 C leveled missions = 1 Free stat
2 B leveled missions = 3 Free stat
1 A level mission= 4 Free stat
1 S level mission= 6 Free Stat