The Tree-based FPGA offers better density and timing determinism than traditional mesh-based FPGA. Moreover, thanks to its multilevel structure, it offers greater easiness to balance dual signals in terms of routing resources number. In this paper, we study the use of the Wave Dynamic Differential Logic (WDDL) on a custom tree-based FPGA of 2048 cells. The WDDL technique offers an effective way to withstand Differential Power Attacks (DPA). However, the effectiveness of this countermeasure is guaranteed provided a symmetry is maintained between the routing of both the direct and complementary paths, which is very hard to achieve in FPGA. Thus, balancing aware Computer-Aided Design (CAD) tools must be developed. In this work, we propose first adjacent placement and balancing-aware routing techniques for tree-based FPGA to counter the routing unbalance. Then side channel analyses are performed on FPGA circuit implementing PRESENT crypto-processor. Experimental results show that the balancing methods enhance the design security against side channel attacks.