Alternate weight is another way to pull an average and if you want to change the calculation but don't want it to affect what is already in the system. Alternate weight can be added in order to add a new weight.
GPA Weight is not necessarily looking at the Alternate Weight, it is a separate item and depending on what you are looking to do, you can set the score with the Alternate weight formula..
In the case of Simple GPA, the weight does not add a bump to the score, but with weighted GPA it does depending on your calculation.
Alternate GPA set up is done in Client Services at the beginning of when a school is setting up their account.