The table in the upper-left contains the list of "Available" skills. Next to the word "Available" is a selection box that lets you pick which "view" you want. It is this view which will be used to determine the structure of the table below it. The same is true for the "Selected" skills which list the skills of your character. By clicking on the Filter icons in the toolbar (the icons with the magnifying glasses) you can filter which skills are included in the table. You can add a rank of a skill by double-clicking on it, right-clicking on it or clicking on it and the on the right-arrow button. You can add more than one rank at a time by right-clicking on it. Similarly you can remove ranks of a skill by double-clicking on it in the "Selected" table, or by right-clicking on it, or by selecting it and then clicking on the left-arrow button above the table. Exclusive skills have a Cost of 0, which means they cannot be purchased. In the House Rules menu you can opt to set the Cross-Class skill cost to 0, 1 or 2. You can also opt to bypass the max rank restriction. As elsewhere in PCGen anything you don't qualify for is in red italics.
The info-pane in the bottom-left will give you details about any skill you click on, including the source of the skill.
The bottom-right section gives you skill-related information about your character. The Max Class Skill Ranks indicates the maximum rank you can have in a Class Skill, and Max Cross-Class Skill Ranks indicates your max rank in Cross-Class skills. You can modify the Cost of Exclusive skills (if it's non-zero it means that Exclusive Skills can be purchased). You can also edit the total number of skill points you have left. At the bottom is a selection box where you can select which class for which you are purchasing skills. To its right is a field indicating how many skill points you have remaining to be spent for that class. The cost of skills may vary depending upon which class you have selected.
There are "sliding dividers" between the skill tables - you can click on this divider and slide it back and forth to your preferred location. There's also a divider between the upper-tables and the info sections below which you can drag up and down to change the viewing area of each. There's another divider between the info sections. This combination of 3 sliding dividers is common to most of the character-related tabs to allow you to change how much screen real-estate is devoted to each section. On most tabs there's a button which has 2 circling arrows that will reverse the orientation of the views between horizontal and vertical. This gives you many options on the layout of the tab.