Because you have new onset of problems (ie neck and upper back tensions) since the introduction of your new desk, you can optimize your posture. Most muscle strain comes from overuse or imbalance, and most office related pain comes from misalignment or lack of core muscle strength.
To figure out what's going on, first, try to get a sense for your posture. You can do this with a mirror or have someone take your picture from 2 perpendicular angles (eg side and back).
Posture impacts all of your muscles, so here's an overview: Feet should be about shoulder width apart with your weight evenly distributed. You should have comfortable, sturdy shoes. Your knees should be slightly bent. Your hips should be level with your pelvis in a neutral position-- not tilted to either side, flexed, or extended. Your core should be tight, with your stomach held in and your shoulders above your hips, and your head should be tilted so that you can see straight ahead.
Monitors should be about 16 to 24 inches away from your eyes-- about arm's length. You should look away from the monitor every 10 - 30 minutes to focus on something far away, and so that your muscles aren't still for too long.
If your arms are not at your side, make sure your core is strong when you hold them away. To use your core, stand with posture as above and hold your stomach and butt in, like a gymnast or an archer. If you don't use your strong core while you stand, you are likely to use your neck to do what your arms should be doing. If your core (abdomen and back muscles) is strong, your neck can just keep your head up, and your arms can move your hands. This is particularly important because you are standing. To prevent soreness, be sure to use your core.
Next, make a list your repetitive activities and log your pain and activities to look for an association. If there is a task you do that correlates with your pain, examine which muscles are involved. Try keeping your core muscles tight while you do it.
You can also ask an ergonomics expert to evaluate you and your environment.
Ten Tips for Improving Posture and Ergonomics
Guidelines to Improve Posture