You may have noticed that connecting the caches to the memory-space can be done separately from defining the caches. It is possible to connect and disconnect the caches at any time during the simulation. You may, for example, boot an operating system and set up the workload with Simics in -fast mode, save a checkpoint and reload it in -stall mode when you want to start cache simulation.
To get decent cache statistics, you should run a few million instructions to warm up the caches before actually starting to do measurements on the cache behavior of your workload. Note that this is only a rough advice; the precise warm-up time needed will depend on the cache model and the workload.