1. Is your business going to grow and remain solvent? If this is the case - some kind of payment agreement needs to be negotiated by you or your tax professional and then later a request to waive penalties can be requested.
2. Is your business destined for dissolution and closure ? If you just can't make your business work - you might consider shutting down. Your professional will help mitigate the damage to you personally. Quite possibly - you personally might avoid any kind of assessment.
3. Do you believe in your business - yet believe you'll need to dissolve your entity and start over? You might have had a bad couple of years but believe your business model has a future. If this is the case just like in example #2 above - you might consider dissolving your entity and starting from scratch with a new entity. Your tax professional will help you mitigate the damage to you personally. You'll just have to be a model business in your next go-around and be sure to be current on taxes.