Set up is key for productive work, it is good to spend a bit of time to do this.
This option allows you to switch between filling in the stroke of the box or actually filling the box itself with a colour, the same can be applied to type. This is how you can create tints of a colour by adding moving the arrow to the left to decrease the percentage then adding this to the swatch pallet.
Just an example of a 75 and 50% tint of a colour and below that the same again but with a spot colour at 100% and with a 75% tint.
An example of how overprint works:
With multiple colours often being used in overprinting it is good to know if there is going to be to much ink on the page, with the use of the ink level option this will give you a warning when there is to much ink on the paper.
Print set up page, trim marks and colour bars are useful and you can enable/disable what ink you want to use in the printer. Its also a good idea to check that any unused swatches are deleted otherwise it can result in unnecessary expenditure due to the fact the printers have to make a plate for each colour you use.