We present a $^{63,65}$Cu and $^{29}$Si NMR study of the quasi-2D coupled spin 1/2 dimer compound BaCuSi$_2$O$_6$ in the magnetic field range 13-26 T and at temperatures as low as 50 mK. NMR data in the gapped phase reveal that below 90 K different i
ntra-dimer exchange couplings and different gaps ($Delta_{rm{B}}/Delta_{rm{A}}$ = 1.16) exist in every second plane along the c-axis, in addition to a planar incommensurate (IC) modulation. $^{29}$Si spectra in the field induced magnetic ordered phase reveal that close to the quantum critical point at $H_{rm{c1}}$ = 23.35 T the average boson density $bar{n}$ of the Bose-Einstein condensate is strongly modulated along the c-axis with a density ratio for every second plane $bar{n}_{rm{A}}/bar{n}_{rm{B}} simeq 5$. An IC modulation of the local density is also present in each plane. This adds new constraints for the understanding of the 2D value $phi$ = 1 of the critical exponent describing the phase boundary.
