Mining and storing your resourcesOf the three resources types metal and crystal are the easiest to extract. First, look at your planets overview on the right hand side of the screen:

You can see next to the small picture of your planet that there are the three symbols for the resources along with a %. This tells you how abundant that material is on your planet, the more of it that is available, the faster you will be able to extract that resource. Resources are infinate, they cannot run out - but they can take a while to extract if the planet has a very low abundance of that resource.
Certain structures have the ability to mine resources from your planet. Mining is automatic, as long as you have a structure on your planet that can mine the resource it will continue to do so without your intervention. The resource will also be automatically placed in the resource pool for your planet. NOTE: resources are per planet, your other planets do not share this resource and must mine their own materials. However, you can send resources between planets with your ships, this will be coevered later when we discuss missions.
As you have just started you have one structure - your "Colony Hub". The colony hub can mine small amounts of metal and crystal, so you should never be in a situation where you are without resources or the ablility to mine them.
How to get exotic matterIn order to get the exotic resource when you first start out you have to research the "Liberty" Extraction class ship and create a fleet (Fleets will be covered below) with your ships. You then have to send that fleet to the nearest gas giant planet on an extraction mission. The ships will mine the resource and place it into your resource pool upon return!
Storing your resourcesAs you saw above, you can see how much of each resource you have available and how much storage space you have. Once your storage space is full for that resource your structures will stop mining it. They will continue when you have made room for more resources by either using some or by increasing the storage space available. Increasing the storage space is easy and can be done in two ways.
1. Build a warehouse OR silo for that resource.
Build a metal silo to store more Metal, build a Crystal silo to store more Crystal and Build a Exotic Silo to store more exotic. When you build any of these structures, the total storage space for those resources will be increased. A warehouse increases storage space for all resources, but can store less compared to a silo. They are very useful however if you are low on available slots on your planet.
2. Upgrade an existing silo structure or warehouse.
Every structure you can build can be upgraded up to a maximum level of 10. As the structures are upgraded they get more health, greater firepower (if it's a defensive structure) and more storage space (if its a silo). Upgrade a silo to enable it to hold more of that resource.
The Colony hub can also store small amounts of resources so upgrading this will also allow you to store more resources.
Next we will talk about how to build and upgrade structures