Interest in the integration of Terrestrial Networks (TN) and Non-Terrestrial Networks (NTN); primarily satellites; has been rekindled due to the potential of NTN to provide ubiquitous coverage. Especially with the peculiar and flexible physical layer properties of 5G-NR, now direct access to 5G services through satellites could become possible. However, the large Round-Trip Delays (RTD) in NTNs require a re-evaluation of the design of RLC and PDCP layers timers ( and associated buffers), in particular for the regenerative payload satellites which have limited computational resources, and hence need to be optimally utilized. Our aim in this work is to initiate a new line of research for emerging NTNs with limited resources from a higher-layer perspective. To this end, we propose a novel and efficient method for optimally designing the RLC and PDCP layers' buffers and timers without the need for intensive computations. This approach is relevant for low-cost satellites, which have limited computational and energy resources. The simulation results show that the proposed methods can significantly improve the performance in terms of resource utilization and delays.