First a detail in the title. d=6 Calabi-Yau spaces are used in d=10 string theory. In d=11 M-theory, to get analogous results, you use d=7 manifolds called G2 manifolds. (If you continue to d=12 F-theory, you use Calabi-Yau again, but now they are d=8.)
There are two classic ways to get gauge groups in string theory. One is to use a stack of branes, and then consider open strings that end on the branes. If there are N branes, the open strings will produce a gauge group of order N, e.g. U(N). See Clifford Johnson's "D-brane Primer" for more about this.
This way of generating a gauge group has no relationship to the Calabi-Yau at all, except in the sense that the brane stack inhabits a submanifold of the Calabi-Yau.
The other way is to start with a big gauge group intrinsic to the strings, and then break it in some way. For example, there are d=10 string theories with gauge groups E8xE8 or SO(32). 1980s string phenomenology revolved around identifying an SU(3) part of one of the E8 fields, with an SU(3)-valued connection on the Calabi-Yau, leaving an E6xE8 grand unified symmetry. The standard model gauge groups were then supposed to arise as subgroups of the E6.
There are still other ways to get gauge groups in string theory, e.g. the d=10 gauge group can be broken by "fluxes"; and
@arivero proposes to use the classic Kaluza-Klein approach to obtain the non-chiral U(3) part of the standard model (obtaining chiral SU(2) from Kaluza-Klein is a problem, and is why it was abandoned).
But as I said, the main ways are (1) brane stacks and (2) embedding a spin connection in a stringy gauge group. Only the latter uses a bundle from the Calabi-Yau, and the bundle is identified with a part of the stringy gauge group that does
not show up in phenomenology... Sorry if this isn't what you were expecting!