This is where all your organization and tool placement comes into play. Here I will show you how I set up my work space, some people may have more room then I have but this is a great setup with little space.
The initial layout of your workspace can make building your model more enjoyable and easier to find the tool you need. If all your tools are laid out the way you like them in an orderly way then it will make finding the right tool easier.
I have two cutting boards/mats, I use an a3 cutting mat for the main model work, and a cutting board (like you would use in the kitchen) for my tools. A must have is a non slip mat under your cutting mat/board so your mat doesn't slide everywhere.
I like having my tool box within reach so I can grab any extra tools that I don't keep on my work desk. They are usually tools like alligator clip stand holder, scissors and pinstripe masking tape. Your tool box should be close at hand but not getting in your way so you can get to your extra tools when needed.
This is how I like to have my work desk layed out, but it may be different for you. I have my mini side cutters, tweezers, and files on my right (as I'm right handed) and a rag for drying my paint brush. I have a minimum of two jars, one for cleaning my paint brush and one for doing my decals. This is a must to keep them separate so your decals stay as clean as possible.
If you keep your workspace neat and tidy you will find making a model more enjoyable. You will also be able to find the right tool for the job and not waist time looking for it. You should also have a good lamp to illuminate your workspace so you don't have a shadow over what you are working on.
I hope this is helpful in setting up your workspace and gives you an idea of how it can be done. This is only an example of how your workspace can be set up and everyone else does it differently.