GPU-embedded systems have gained popularity across various domains due to their efficient power consumption. However, in order to meet the demands of real-time or time-consuming applications running on these systems, it is crucial for them to be tuned to exhibit high performance. This paper addresses the issue by developing and comparing two tuning methodologies on GPU-embedded systems, and also provides performance insights for developers and researchers seeking to optimize applications running on these architectures. We focus on parallel prefix operations, such as FFT, scan primitives, and tridiagonal system solvers, which are performance-critical components in many applications. The study introduces an analytical model-driven tuning methodology and a Machine Learning (ML)-based tuning methodology. We evaluate the performance of the two tuning methodologies for different parallel prefix implementations of the BPLG library in an NVIDIA Jetson system, and compare their performance to the ones achieved through an exhaustive search. The findings shed light on the best strategies for handling the open challenge of performance portability for major computational patterns among server and embedded devices, providing practical guidance for offline and online tuning. We also address the existing gap in performance studies for parallel computational patterns in GPU-embedded systems by comparing the BPLG performance against other state-of-the-art libraries, including CUSPARSE, CUB, and CUFFT.