I would do a flush with old lines, but it's up to you and what you have done already (I wouldnt worry about it much).
You would be adding fluid to keep the reservoir topped off as the car idles with the return line vented into a bucket. Having an assistant there to shut the car off is nice.
When the fluid coming out of the return line looks clean, you should be getting close to done.
Check your repair manual or the instructions with your pump - both might have some info to help.
Good luck.