Rates have 2 purposes: To help you budget for work, and to track the billable value of work. All rates are hourly.
An admin user can access the Rates list from the Administration screen:

A rate must have a title, hourly charge amount and a reference table (where it can be used). You can create a rate that is usable everywhere using the "Reference table : Any" option. The other reference options are outlined below.
When you edit a staff (user) record, you can select a rate for that staff member. The picklist will only show rates from the full rates list that have a "staff" reference. The advantage of this is that when changing rates, say for your senior consultants, you only need change the selected rate in the Admin rates list.

Note that a staff members rate is only applied if the record they are logging time on is set to use Staff Rates.
For example, a $2000 line item (or component) for 'design' work might entail 10 hours work at a rate of $200/hr - you might consider this a premium rate. However, a 'training' component might also have 10 hours budgeted, but your charge out rate for training is typically $150/hr, so this line item comes to $1500.
So before you start creating a job and the components for it, you should define the service rates you might need.

You can define system wide default rates for Issues, Components and Jobs. For Contracts, you can configure the default rate for a contract type under the Contracts administrative options.
When you setup an Issue, if the issue progression allows it, you will be able to choose from one of the general rates or the issue specific rates.

As work is logged on an issue, the billable amount will be tracked under the Time Allocations section:

Note that a period of work on an issue may be associated with a contract, in which case that block of time will use the rate for that contract.
If you change rates whilst a time allocation is still open, any activities in that period will be updated. However, activities for a time allocation which has already been invoiced, packaged or freed will not be changed - they will retain the previous rate.
Once a rate has been used, you can only de-activate it. Click the name of the rate in the rates list in admin to set it inactive. Once inactive, the rate will not be usable for new work, but existing activities with this rate will retain this rate.
A rate that has not been used may be deleted by clicking the recycle bin on the far right.