You can use tools even if you are not skilled with them, but your unfamiliarity with the associated skills needed to effectively use the tool will make any tool checks made with the tool more difficult.
In general, each tool has a number of things they may be used for. A Poisoner’s Kit can allow you to effectively make, mix and apply poisons, and a Thieves Kit comes with lockpicks and a torsion wrench, which is all that is needed to open any standard lock. To mix a deadly poison, or to lockpick a door open, you would need to make the appropriate tool skill check to complete the task, unless your Gm decides it is not necessary for you to roll. (Performing the utmost basic functions of a tool generally falls under this, such as applying a poison with a poisoner’s kit.)
Tool skill checks are performed with tools by performing a special skill check that also includes any bonuses that apply to the tool, such as skill points you have spent on the tool. For instance, a check using Smith's Tools might have you add both your Endurance skill bonus and your Smith's Tools bonus to the roll.
You can use tools to create or craft items, if possible.
You can spend money to collect raw materials to craft the item with. Half of the value of the item you are crafting is needed in raw materials. For example, you would need 5 Gold worth of materials to create an item with a value of 10 gold.
To successfully craft the item with your tools, you make a tool skill check and you must succeed a DC set by your GM, depending on the difficulty of the item you are creating. Your familiarity with the tools and the skills associated with the craft you are performing may also affect the DC, for example.