You will probably need to remove the baseboards and shoe molding before you lay the new floor. The old baseboard and molding may suffer some damage during removal. Replacing it will let you choose the look you want. If you plan to let the wood show, you should choose trim of the same species and color as your flooring. Another option is to paint the baseboard and shoe molding before installation. This frees you to select a complementary color without worry about matching the flooring. Another benefit of choosing paint over stain is that you can paint the doors and trim to match the baseboards.