Your net profit from Schedule C is treated as ordinary income while your loss from Schedule E may be limited by the passive activity loss rules. If that is the case, then your Schedule E loss will not offset your Schedule C net profit.
Schedule B, among other things, is used to report interest and dividends. Schedule D is used to report short-term and long-term capital gains. The federal income tax is different depending upon the type of Schedule B income and Schedule D gain (e.g., interest versus qualified dividends, short versus long term capital gain). Regardless, the income/gain from both would be factored into your tax liability.
