I'm new to tandem riding and am the stoker. I have a lot of single bike experience and have a good single bike fit. On the tandem, when I stand, my knees sometimes hit the handlebars. I plan to change to a set-back seatpost but I think the standing position is really more affected by the handlebar position. If I move them up I will be sitting too upright. Any stoker position advice?
Move the bars forward to try and get them in the same place as your single bike. But unless you are quite short they will still be closer as tandems don't normally have enough length in the back to achieve this. More than likely you will have to change your out of the saddle technique and not move so far forward.
Do you and your captain stand at the same time? If not, the captain's back will prevent you from leaning forward and moving your hips back. You can ask the captain to move to the drops to give you little more room while you stand.
Which part of the handlebar are your knees hitting? If it is the drops, I can think of two solutions which might help. First, consider wider bars. The stoker bar on our tandem is quite a bit wider than the bars on my single, and I think this may keep you from hitting your knees if the drops are the problem. The other solution (again if it is the drops you are hitting) might be to change to a bullhorn style handlebar that doesn't have drops. I am the stoker on our co-motion speedster, and have their adjustable stoker stem, which has worked really well for me. The adjustable stem may give you more options with regards to moving the handlebar height and not becoming too upright.
If I move them up I will be sitting too upright. Any stoker position advice?
You are right in that your saddle position has nothing to do with how you ride out of the saddle. It's all about the distance between the bottom bracket and handlebar and handlebar height relative to saddle height + crank length to a lesser extent.
How tall are you and what's your insteam?
What year, make and model tandem do you have?
Have you checked your saddle set-back / bar height / crank axle to handlebar dimensions on your single bike against the tandem's to see how the compare?