  Heavy flavor and quarkona production are important hard probes to test the
Quantum Chromodynamics (QCD) and measure the properties of the Quark Gluon
Plasma (QGP) created in high energy heavy ion collisions. The new PHENIX mid-
and forward-rapidity silicon vertex detectors provide precise Distance of
Closest Approach (DCA) determination, allowing charm and bottom yields
identification, and improve di-muon mass resolution for charmonia studies. The
relative $\psi(2S)$ over $J/\psi$(1S) yields measured in $p$+$p$, $p$+Al and
$p$+Au data at $\sqrt{s}=$200 GeV help us to understand final state effects on
the charmonia production. Direct access to B-meson production has been enabled
via measurements of non-prompt $J/\psi \to \mu^{+} + \mu^{-}$ in $p$+$p$
collisions at $\sqrt{s} = 510$ GeV and Cu+Au collisions at $\sqrt{s} = 200$
GeV. The fraction of B-meson decays in J/$\psi$ yields in the $p$+$p$
measurement agrees with higher energy results from Tevatron and LHC. This
fraction is enhanced in Cu+Au collisions suggesting the B-meson yield is not
modified by the medium whereas J/$\psi$ is strongly suppressed.
