How long has your tank been up and running for? If you have brown algae, this is diatomic algae and is generally a good sign that your tank is doing what it should be. Generally, once the tank stabilizes, it disappears on its own, however it may never go away entirely, this is where your CUC will help.
If you want your hitchhikers to survive, you'll need to do a type of cycling called soft cycling. This is, doing some small water changes to help keep harmful substances down - although this will slow your overall cycling period down. My recommendation is to just hard cycle and let whatever will die, die. If it survives then congrats. ;)