We investigate the mixed state properties in a type II multiband superconductor with uniaxial anisotropy under the Pauli paramagnetic effects. Eilenberger theory extended to a multiband superconductor is utilized to describe the detailed vortex lattice properties, such as the flux line form factors, the vortex lattice anisotropy and magnetic torques. We apply this theory to Sr$_2$RuO$_4$ to analyze those physical quantities obtained experimentally, focusing on the interplay between the strong two-dimensional anisotropy and the Pauli paramagnetic effects. This study allows us to understand the origin of the disparity between the vortex lattice anisotropy ($sim$60) and the $H_{rm c2}$ anisotropy ($sim$20). Among the three bands; $gamma$ with the effective mass anisotropy $sim$180, $alpha$ with $sim$120, and $beta$ with $sim$60, the last one is found to be the major band, responsible for various magnetic responses while the minor $gamma$ band plays an important role in the vortex formation. Namely, in a field orientation slightly tilted away from the two dimensional basal plane those two bands cooperatively form the optimal vortex anisotropy which exceeds that given by the effective mass formula with infinite anisotropy. This is observed by small angle neutron scattering experiments on Sr$_2$RuO$_4$. The pairing symmetry of Sr$_2$RuO$_4$ realized is either spin singlet or spin triplet with the d-vector strongly locked in the basal plane. The gap structure is that the major $beta$ band has a full gap and the minor $gamma$ band has a $d_{x^2-y^2}$ like gap.
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