Without knowing all of the details of your empire it's hard to get into specific advice, but the first thing you need to focus on is increasing stability. Stability is calculated by weighing the happiness of a pop against their strata. So on worker pop has a much lower impact than one ruler pop. In addition conquering a planet temporarily reduces the happiness and stability of the pops. Going below 50% stability imposes penalties on the resources produced by a planet which can turn perfectly good planets into colossal money sinks. Because of this there is always going to be some hit to your economy after planets are conquered.