Should I let my employer change my status from employee to independent contractor now that I moved out of state and work remotely?

I used to live and work in Idaho for a medical office. I moved to Colorado and continue to work for them remotely from home. We are trying to figure out taxes and my boss said his accountants told him it is easiest to switch me to an independent contractor (1099 vs W2 employee). I think this may just be easier for them and not for me - what do I need to consider and what other options would I have? I have done a little research and it sounds like I will have to pay my taxes all at once and end up owing money instead of getting a tax return each year? 

I do not want to agree to something I am not comfortable with, this is not my area of expertise - are there any other questions I should be asking? Other ramifications I need to be aware of? How difficult will filing my taxes be compared to just using a W2 (as I always have in the past, using TurboTax - never any issues or complications).