2 Units in one documents

When I draw a line with units 2 and then measure it, it shows a much larger number. If I have a dimension annotation and I draw a line with the same number, the new line will be much longer.
Not sure how to fix this. Any advice is appreciated.

It sounds like you are not using the Length or Distance analysis commands to check the objects.
Are you creating a dimension instead?
Dimensions belong to named Annotation Styles and they can be setup to use multipliers and generate what you described.
The analysis commands do not.

Beyond that overview, to understand your particular issue, we will need an example file.