Without any images or files, it's anyone's guess.
Here are some general guesses:
1. Simple setup: when I'm using segmented art, I usually create a layer with circle the size of the joint with a smaller circled scaled down to the center as a guide for the region between the upper and lower limbs. The outer circle gives me a guide for making the ends match during the bend, and the center point gives you a reference for where the bones should connect. If I do this carefully, I can get nice bending joints in my puppet.
2. Intermediate: Moho has a neat feature called Smooth Joint. Just select the two bones you want to use for the joint and apply Smooth Joint. IMO, this works better with bitmap images--in fact, it works surprisingly well for many situations with bitmap art.
3. Advanced: Use Smart Bones. if you're using a single drawing for the limb, make sure your points are distributed for nice deformations. A Smart Bone Action can be used to correct any bad deformations.
4. Really advanced: Lately, I've been creating more vector-based rigs than bitmap, and relying more on Point Binding than Flexi-binding. It really depends on the designs for the character and what they need to do. These days, a combination of Point Binding and Flexi-binding has been working out best in the shows I'm working on. Also, I'm using a technique I learned from Victor, where an 'elbow' or 'knee' bone can be used to help hold the volume of the joint when it bends. Basically, this is a short bone attached the the upper limb, and using Angle Control Bone pointed to the lower limb and set to 50% of the rotation. If you point bind the knee or elbow points on either side of the limb, the small bone will maintain the 'thickness' of that joint. I think Victor's 
Rubber Hose tutorial illustrates this 'joint holding' technique. For more complicated designs, I may still use a Smart Bone Action on top of this trick to get the exact deformation I need. Typically, the Action will make the inner point of the joint a Peak during the bend, and smooth it out again when the limb extends.
Hope this helps.