Generally speaking, with configurable products you assign the main price based on the lowest combination of option selections. Each option is given a price modifier, and the sum of the options is added to the base price to make up the final price.
For example, let's say I sell a mattress that comes in Full, Twin, and King sizes and has the choice of either inner springs or memory foam. I know that the Full mattress with inner springs is the cheapest option I sell, so I set the base configurable product price to $199. I also know that memory foam costs $100 more than inner springs, so I set the inner spring option to $0 and the memory foam option to $100. I know that Full is the base size, so I set that option to $0, Twin is $25 more so I set that option to $25, and king is $50 more so I set that option accordingly.
Using these settings, a King-size memory foam mattress should cost the customer $349.