A very general question gets a very general answer...
In chromatography, there is always going to be a mobile phase and a stationary phase. The mobile phase is the moving component of the system and the stationary phase is the non-moving component of the system. You dissolve your substance in question in the mobile phase, and then the mobile phase travels through the stationary phase, propelled by some force. The basic principle of chromatography is that different substances have different levels of attraction to each of these phases, primarily because of differences in polarity. Substances more attracted to the mobile phase tend to move further during the chromatogram, and substances more attracted to the stationary phase tend to move less. Based on the separation, you can make determinations about the main substance and its component substances.
In a simple explanation of paper chromatography, a piece of paper treated with your main substance in question is dipped into a pre-determined solvent, which causes the solvent to travel up the paper due to capillary action. The components of your main substance are carried with the solvent to different extents based on their properties and leave "spots" on the paper. In this system, the paper is the stationary phase and the solvent is the mobile phase. The important measure of the chromatogram is exactly how far each of the component substances moves, or how far the "spots" are from the baseline.
If you do not achieve the desired separation through your first attempt at paper chromatography (you see two "spots" when you know you should see three), then you can take one of two actions: you can change the stationary phase (the paper) in your system, or you can change the mobile phase (the solvent) in your system. There are several different types of chromatography paper which lead to different separations, based on the substances in question; additionally, there are numerous solvents and solvent mixtures which will also change the separation. You make adjustments to your system until the desired separation is achieved.