The demand for high-fidelity numerical simulations in soil-structure interaction analysis is on the rise, yet a standardized workflow to guide the creation of such simulations remains elusive. This paper aims to bridge this gap by presenting a step-by-step guideline proposing a workflow for dynamic analysis of structures with pile foundations. The proposed workflow encompasses instructions on how to use Domain Reduction Method for loading, Perfectly Matched Layer elements for wave absorption, soil-structure interaction modeling using Embedded interface elements, and domain decomposition for efficient use of processing units. Through a series of numerical simulations, we showcase the practical application of this workflow. Our results reveal the efficacy of the Domain Reduction Method in reducing simulation size without compromising model fidelity, show the precision of Perfectly Matched Layer elements in modeling infinite domains, highlight the efficiency of Embedded Interface elements in establishing connections between structures and the soil domain, and demonstrate the overall effectiveness of the proposed workflow in conducting high-fidelity simulations. While our study focuses on simplified geometries and loading scenarios, it serves as a foundational framework for future research endeavors aimed at exploring more intricate structural configurations and dynamic loading conditions