How do you get contents of large flask into a smaller separatory funnel? Separatory flasks that I use have a ground glass joint, but it is not clear how that joint is to be used. Videos I have seen just show people pouring stuff into the throat of the funnel.

Normally the situation I have is that the solution is in a large flask, maybe a 1000ml flask, and I need to separate a thin layer of the solution that is at the bottom of the flask using a 500ml separatory funnel. The question is how to get the bottom of the flask to the funnel.

Saying "oh just use a bigger funnel" is not a solution, because the flasks, reactors and carboys I have tend to be significantly larger than any normal separatory funnel. For example, if I have a 3000ml reactor or 5 gallon carboy with a solution in it, I am not going to go looking around to spend hundreds of dollars on a gigantic 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.