When you start the jump to another system, ie when the count down begins, just set the throttle back to zero. When you enter the new system you will be at idling speed in super cruise, which is about 30kps and is practically akin to being at a standstill. You should then be perfectly safe for a good long while whilst you figure out where you're going next.
When you jump, it increases the heat build up in your ship. So if you're next to a star and your heat is already quite a bit up, sometimes initiating a jump can push your heat up over the safety limit. So before jumping try and fly away from the star for a short distance first until you notice your heat levels start to drop before initiating a jump. Some ships are much better than others at managing heat levels. The Lakon trade ships are quite bad at heat management for instance and you need to watch your levels carefully around stars. The Cobra and Diamondback Explorer on the other hand have excellent heat management and you can often jump more or less straight away whilst still next the star you just arrived at.
When your heat gets over 100% you will take module damage, over 150% your ships hull will start taking damage.