Ideally, preloaded bolted connections are design such that the total load seen by the bolt is the preload. If the joint is overloaded, the joint will separate and the bolt will see the additional load. If the joint has significant flexibility the bolt may also see additional load due to prying or some other effects. Most of the time the bolt preload is very close to the bolt proof load (85%). The preload is important for controlling the stress in the bolt and the stiffness of the joint.
It is possible to create a simulation model of a preloaded bolted joint that includes the effects of preload as well as external loads (link to Preload Bolted Joint). This type of model is sometimes useful if you need to look at detailed joint stress or require accurate joint stiffness. However, this type of model can require a great amount of compute time and may not provide the information you need to calculate factors of safety since the minimum stress you calculate may be end up being the bolt preload stress.
In most design scenarios it is not very useful to calculate the bolt-preload stress. This will not tell you how close the bolt is to being overloaded except by increasing the load until the bolt proof load is exceeded. Since this is nonlinear, it may require much iteration. There is no sense in making a science project out of something that may only require a simple model. The most pragmatic approach in many design cases is to ignore the bolt preload stress and calculate the amount of load that each bolt may carry without preload. This could then be compared to the bolt preload to calculate a factor of safety. There are various ways to model this and most will require far less compute time than modeling the actual preloaded joint. A few methods for bolted analysis are listed below.