It's possible to work with both budgies at the same time, at this point you don't need to separate them because most likely they look for each other for comfort and support.
Before you have started to hand feed them, did you first work on making the first connection with them, by using your voice and by making them used to your presence?
From your description and given the time you have had your budgies, it seems that you have moved too fast in training, the foundations of trust aren't yet established and that's why your budgies freak out when they see your bare hand.
At this point, I think it would be best for you to not place your hand on the cage as that is clearly stressing your budgies out and to start all over again, by sitting close to the cage and talk to them in a calm, positive, encouraging and reassuring way. You should only take a step further in training when your budgies are perfectly at ease when you interact with them and when they show actual signs of being receptive to you (by getting closer to you while in the cage, making eye contact with you, etc). Once this happens you can start by offering a little treat in between the cage's bars and get them used to seeing your hand before you actually place it inside of their cage to teach them the step up command.
If you haven't done so already, check the information on the stickies at the top of the Taming and Bonding section's main page.