In the initial Wet your Hands mission, things get a lot easier if you are holding back on units and start out by investing into your infrastructure. Only when you have a good economy, all supply depots and fighter factories you should actually invest into ships. That way, you are in a much better shape of defeating the incoming raiders and rebuilding your losses.
The mission Cpt. Medison can be a challenge. In that mission, you are given a small task force and need to infiltrate the alien space station with ground troops from your colonization ships, free the Cpt. And escort her back to the jump gate you entered from.
This can be difficult as you cannot tackle on the enemy head on with your task force.
The best way to solve this mission is to take over Dead Planet to the left with your forces to give you a bridgehead. Then send over your colonization ships to the space station (marked with a blinking dot on the minimap) to infiltrate it.
In the meantime, build up the infrastructure on the planet and distract the enemy forces they will be sending over from Drye. If you're losing ships, replace them from the planet you invaded, usually bombers work best.
Free the captain and bring her back to the gate. Also make sure the gate is not attacked and destroyed. With the Dead Planet under your control and you reinforcing from there, the mission should be a lot easier.