Below is a link to a resource I provide my investors. The 50 questions are specific to product design/development but the 15 categories are questions that apply to any industry.
If you can answer these questions about your deal you will have gone a long way to avoiding the common pitfalls in the product commercialization process.
Once you have answered the questions for your deal if you'd like to call me I can evaluate your answers, educate you on what strategies are available that would be the best fit for you, and then help you execute your strategy.
Both the founders should have clarity with regards to ownership of the technology, product, corresponding IP (patents, trademarks) and terms of licensing.
One way is to assign all rights to the company, file all patents, trademarks on behalf of the company, and the execute licensing agreement as a legal entity (company) and not individually.
With a view to safeguard interest of each co-founder, you can also execute co-founders agreement among yourselves that will define all terms of collaboration, and what will happen in case one founder decides to exit midway.
Hope this is helpful. For further advice, feel free to get in touch.
Patent costs are ongoing and somewhat variable, so be sure you each have a clear understanding of the costs so you can share them fairly as time goes on. The initial preparation and filing is significant, but so are maintenance fees, foreign filing costs, etc.
The most common pitfall I see is that both people don't want to pay for later stage work that is required and the person not paying still wants their 50% of the patent profits. Be clear as to what happens in case of bankruptcy, non payment, etc.