Items in your Pricebook contain a field that allows you to enter the cost of that item. For a part item, the cost would be the amount you generally pay for that part. When adding cost to a Task item you will enter the expected total of the parts and materials needed for the job in the Material Cost field of the task item. When that part or task item is included in a sold proposal, the cost of that item will be added to the total job cost.
The material cost can be modified individually at the proposal level to account for cost changes however this can only be done by a user with Admin permissions from the Pointman website.
To change the material cost, simply go into your PriceBook items, select the record that you want to modify, and enter in new cost.