Physicists have no serious problem with the anti-matter theory. The only signicant question under study is the very slight difference which leads to a universe made up of matter. If the difference weren't there, we (and the earth, sun, etc.) wouldn't be here.

As far as quarks, they have "color" and electric charge. Ordinary matter (protons and neutrons) is made from the two lightest called up and down. Up has a charge +2/3 while down has -1/3 (in terms of the electron being -1). A proton is made from 2 ups and 1 down, while a neutron consists of 1 up and 2 down. To get anti-proton or anti-neutron, use anti-up and anti-down quarks (which have opposite signs from the ordinary quarks) in the same formulation.