Perhaps you are referring to the FEA or CFD working files? The "jumble" is unavoidable if you are referring to the creation of the files. So, it is best to keep them with the SW model (there are global Simulation Options and Local Simulation options to tell it to save results with the model). We routinely do this on a copy of the CAD database that is moved to a dedicated working directory for obvious reasons. It is a good idea to setup a partition dedicated to FEA or CFD - or even another drive on the same machine, but keep everything together. If the CAD model and "jumble" of FEA files are separated by drives or computers over a network, that can cause voluminous problems esp. during solution because of the network traffic generated from solver read/write operations (esp. with CFD transient, and Simulation transient, dynamic and nonlinear time-step writing of results). Best to keep everything together, and local.