In choosing whether to work with a travel guide or book your own lodging, I have learned from three months of experience that it's important to know yourself, What kind of traveler are you?
If you are independent and don't like the idea of pre-payment or having the guides fees wrapped into a total amount for the whole trip, then it is probably better to make your own arrangements.
Guides have working relationships with lodging operators, who as business owners are trying to minimize risk and uncertainty, hence they favor pre-payment. If you are independent and want to stay flexible, it's probably better to make all of your own arrangements. However, if the whole idea of doing this scares or overwhelms you, then it may be best to use a professional. I have found that trying to walk a middle ground can be difficult.