How do you get contents of large flask into a smaller separatory funnel?
You should proceed as follows:


Charge the funnel with the mixture until it is almost full. 
Let the content settle. 
Separate the lower phase. 
Separate the upper phase. 
Repeat until you have processed all the mixture. 


The ground joint is to close the funnel hermetically. 
This is necessary when you need to perform an extraction. 
A liquid with a mixture of components is charged in the funnel and an immiscible liquid is added. 
The funnel is closed with a stopper and it is vigorously shaken. 

BE VERY CAREFUL BECAUSE PRESSURE CAN DEVELOP INSIDE THE FUNNEL. 

It is better to shake a bit first, take off the pressure, shake again, etc. 
To release the pressure, put the funnel upside down and open the valve. 
Put the funnel upright and let settle. 
When there are two clean phases, release the stopper and take them out separately. 
The components will be distributed between the phases in different quantities, so it is a way to purify those substances.