Scan your pencil drawing into a bitmap format (like jpg) and then use the "Trace Bitmap" feature of the Inkscape open source vector drawing program to turn that into a vector drawing (such as an svg or dxf).
This will give you an initial digital representation of your design.
From there you will need to familiarize yourself with inkscape's tools to correct the drawing, scanning and conversion errors which will inevitably occur. For example, you will want to remove the extra vector anchors which faithfully captured the slightest irregularities in what you thought were straight lines. Truly straight lines should be represented in your drawing by two vector anchors only (one at each end). You will also want to fix all of your "nearly 90 degree" hand drawn angles so that they are precisely 90 degrees. This editing will take a long time if you are new to inkscape but will get easier over time.
Once your vector drawing meets your quality standards, you can make future modifications and print out folding diagrams from within inkscape, without further use of manual (pencil & paper) design techniques.
One nice side effect of converting your drawing into a cleaned up vector image is that you can then modify it's scale proportionally, allowing you to produce your box in any size desirable. You can also then import your saved vector image file into the control software of a vinyl cutter (like the Silhouette) or a laser cutter, either of which can cut out fold-ready boxes out of different materials.