The position of the cranks is normally referred to as being "Out of Phase" (OOP) or "In-Phase" (IP). In-Phase means of the crank arms are parallel with each other. Out-Of-Phase (OOP) means the cranks are off-set by a predetermined number of degrees (e.g., 90°, 180°). The advantages are, no 'dead spot' in the pedalling cycle, i.e., when the captain's cranks move through 5 to 7 / 11 to 1 O'Clock where power output is the lowest, the stoker's cranks are moving through 1 to 5 / 11 to 7 O'Clock where power output is the hightest. In theory and in practice for folks who adapt to it, it's a more efficient way of smoothly delivering max power to the drive train. The down side is, it's far more difficult to stand and sprint or climb out of the saddle since the captain and stoker's upper bodies will be moving "out of sync" as well. The captain also needs to be mindful of his or her pedal position if they intend to corner fast (leaned over) and when going over speed bumps / obstructions so as not to slam the stoker's feet into the ground/obstruction. For teams where the stoker is significantly less stronger than the Captain, some teams find it helpful for the captain to run his cranks just a few teeth out of phase and ahead of the stoker's cranks. This let's the captain begin the power stroke ahead of the stoker. Let me end this part of the discussion by saying, IP vs OOP is one of the more hotly debated tandem topics that you'll encounter among the enthusiasts. However, I would hazard a guess that less than 5% of tandem owners ride OOP which may have more to do with the aesthetics than anything else; it could be said that OOP teams look like taffy pulling machines going down the road.
Adjusting the sync chain:
Drive train maintenance and adjustments are best done with the rear end of the tandem lifted off the ground, e.g., being held with the stoker's seatpost fastended to the clamp of a bicycle workstand and the front tire of the tandem still resting on the ground. This is the "normal" way to hold a tandem in a workstand. If you don't have a workstand just sling a rope around something overhead and create a loop around the stoker's seat/seatpost. Take up enough slack to lift the rear tire an inch off the ground. It's not perfect, but it's better than nothing.
To adjust phasing, you just loosen the eccentric. The eccentric is the cyclindrical aluminum part that the bottom bracket is installed in which, is turn, is installed and rotates in the oversized bottom bracket housing for the captain's cranks. Of course, like most things regarding tandems, there is no standard eccentric design and they all are adjusted a little bit differently. I'd recommend that you take a moment to read through this Web page at Sheldon Brown's site as it does an excellent job of explaining quite a few things that you will eventually want to know about your sync/timing chain and eccentric.
OK, now that your eccentric's loose, rotate it clockwise or counterclockwise to remove the tension from the timing chain connecting the front and rear cranks. You "should" use a Park pin spanner (#1, Green handle) to do the rotating (and hopefully your dealer sold or gave your one; $7/ea) but if you don't have one you should be able to move it by pinching the eccentric between your left and right thumb and index fingers from the bottom of the bike. You'll want to create enough slack in the chain to allow you to remove it from the front chain ring. Once it's off, line up the crank arms so they are roughly horizontal with the bottom (aka, boom or boob) tube and then slip the chain back on the top teeth and turn the crank forward to walk the chain back onto the chain ring. If the crank arms are not exactly horizontal, before adjusting the chain rotate the eccentric to remove the slack just to be sure how far off they are. Then, rotate the eccentric to loosen the chain again and then move it forward or backward on the front chain ring the right number of teeth to get the front crank lined up with the boom tube and rear crank. Once you have the cranks lined up with the eccentric rotated to take all but about 1/2" of the slack out (you want some slack) , re-tighten the fixing bolt(s) for your eccentric and you're done.