Shipping configuration

I am so confused by the shipping options. I thought I had it set up somewhat accurately by adding my commonly used packages. However, now I’m getting ripped off. Someone orders a sample along with an item that ships in a flat rate box and they only get charged 50 cents shipping for the entire order. I need someone to help me figure out what’s wrong. I’m so frustrated I’m willing to pay you for your time if you understand how to to configure this correctly. I’m an IT professional but this is making my brain hurt. When I had it set up very simple with one package type it was more accurate but occasional over charges which I refunded.