CBSubs doesn't have negative balances. The best I could suggest is subscribe them as Expired. Then set your plans to renew from expiration date by setting "Manual renewal extends expiration date as follows" to "Renewal extends expiration date (without gap or overlap)" on the Pricing tab of your plans. This would force them to renew for past time (so basically somewhat like a negative balance) when they go to renew.

You could create a CB field for the amount they still that's past due (store it as a negative about... e.g. -50). Then use CBSubs Promotions to add that field to their next purchase of that plan. This will increase the amount of the subscription by that amount. You could then use CBSubs Fields to set it to 0. I'm sure there's also other creative ways to implement what you're needing, but since you've had pricing changes it makes it more difficult.