1. The present continuous is mainly used for fixed arrangements. For example:
I'm meeting my friends at 2 p.m.
She's having her operation tomorrow.
We're flying to Paris next week.
In most cases, there are other people involved in these arrangements - the friends, the hospital, the airline etc. The meeting with friends is definite, and the operation and the flight have been booked.
2. The 'going to' future tends to be used more for things which aren't arranged, for example:
It's going to rain this afternoon.
Listen carefully. I'm going to tell you something important.
Don't eat all that chocolate. You're going to make yourself ill.
As you can see, none of these things are arrangements, so you have to use the 'going to' form rather than the present continuous.
Here's a tip - if in doubt, use the 'going to future'. In the first set of examples, it's possible to use 'going to' :
I'm going to meet my friends at 2 p.m.
She's going to have her operation tomorrow.
We're going to fly to Paris next week.
These sentences sound less definite, but they are still correct. However, the present continuous future cannot be used in cases where the 'going to' future is required. For that reason, the 'going to' future is a much safer choice.
I hope that helps.