Setting Gaia up to use your own textures is generally a fairly simple and fast process.

  1. Create a duplicate of your Gaia Resources file (select it, hit Ctrl D). 
  2. Create a new terrain using the new resources file with Gaia - you need to select it in the Gaia Manager. 
  3. Update the textures, grasses, trees in the new terrain to whatever you want (i.e. physically add them / swap them in your terrain object using standard unity workflow)
  4. Apply these back into your new resources file by selecting it and clicking 'Get Resources From Terrain' (see image below).
  5. Update the spawn rules in your resources file if you need to. If you don't the old ones will be retained. (The visualizer is an awesome tool for doing this)
  6. All new terrains created with the new resources file will retain the new settings.

For video tutorials on how to do this and manage resources in general please check : 

Introduction :

Visualizer :

Terrain Texturing :

There are many video's on this and other topics available here: