Will I end up "unbalanced" if I only wear insoles in one shoe and not in both?

Even if you only have pain in one foot, you should wear your insoles in both shoes. Wearing an insole only in one shoe will raise one side of your body slightly, and may put your body out of balance, cause back pain, joint discomfort, or change the alignment of your hips.

It is likely that your symptoms of pain in one foot are due to global mal-alignment of the feet, legs and lower back. It is important to try to create symmetry in the body through orthotics for both feet at the same time. Using single footed orthotics or insoles could worsen alignment and aggravate symptoms. Hip or knee pain has been reported in people who place something as small as a piece of thin material in their shoe to provide cushioning to their sole. Even something thin can have big implications on the body. 

Stretching shorted muscles that could be contributing to the mis-alignment will be a helpful and cost-effective way of managing your symptoms. Stretching focused on alignment and mobility equally between the left and right sides of the body is important. You might benefit from custom orthotics as the product accounts for sensitive areas on the foot by providing more cushioning, while creating alignment in the feet while weight bearing during walking, standing, or running activities. This may be your best option for relieving your foot pain and preventing further injury.

It's great you're getting results by using just one insole. But as you've guessed, you may cause more problems for yourself this way. Using one insole will throw your body out of alignment and may cause pains shortly. It may be better for you to use both to keep you prevent joint pain due to malignment.