This paper proposes a methodology to access data and manage the content of distributed memories in FPGA designs through the configuration bitstream. Thanks to the methods proposed, it is possible to read and write the data content of registers without using the in/out ports of registers in a straightforward fashion. Hence, it offers the possibility of performing several operations, such as, to load, copy or compare the information stored in registers without the necessity of physical interconnections. This work includes two flows that simplify the designing process when using the proposed approach: while the first enables the protection or unprotection of writing on different partial regions through the bitstream, the second permits homogeneous instances of a design implemented in different reconfigurable regions to be obtained without losing efficiency. The approach is based and has been physically validated on the ZYNQ from Xilinx, and when using partially reconfigurable designs, it does not affect the hardware overhead nor the maximum operating frequency of the design.