Modeling raised pads at bolt locations to connect parts together is relatively simple and can provide a good approximation of joint stiffness. It does not make it very easy to estimate bolt loads or stresses however. This method does not address the issue of bolt prying in the joint. The pads should be approximately two bolt diameters with a thickness of 10% or less of the bolt diameter.
This method is based on the observation that most preloaded bolted joints will have good contact around an area of about two bolt diameters at each bolt. In between bolts there may be contact but actual stiffness will depend on many, sometimes uncontrollable, parameters such as surface finish, flatness and friction. It is generally more conservative to ignore contact between bolts unless some techniques are used to ensure good contact. Common techniques may include the use of Locktite, glue or oil between the interface surfaces to fill the small voids. If these techniques are used you may be able to justify ignoring the bolted connection (see Ignore Bolts).
The very local stresses around the bolt locations will not be very accurate however the stress and deflection away from the local bolts areas should be good.