Part of your income being self-employment income should not be a problem. You just turn in two years of tax returns. If you run a lot of your expenses through your company, you probably need a very experienced loan officer with a good broker / banker company. The loan officer will also need the financial statements from your company if you run a lot of expenses through your business.
Your situtation sounds complicated enough that you don't want any "order taker" type, inexperienced loan officer to help you get your mortgage. I have two very solid lenders I can recommend if you'd like to contact me.