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The game auto saves on every rebirth and a few patches ago it started saving every 5min. Sorry for the lost days. The game also has offline progress now, which should help going forward.

You can also save by going to the Menu Options (top left) and then the Save Menu.

There are 3 ways to train skills.
1) Everything trains at the same time - done by default or when using the train all button at the bottom right.
2) Train a specific skill - done by pressing the 'Train' button next to a skill.
3) Queued training - done by setting the value you want to train a skill to in the 'Next at' field - by default this is set to 0