When doing UX for data vis, the actual data matters.
For example when showing bar charts with data that you want people to compare, your wireframes need to clearly show that the Y axes should have the same maximum and minimum values.
Another example: if you have two bar/line charts where the Y axes have the same minimum and maximum values, they're best presented in a row next to each other. This makes it easy to compare between them because the same height represents the same value on both charts.
To be honest, I haven't found a UX tool that's good for prototyping for datavis, since you can't import data into the stock graphs, but that data is vital to determine a usable layout.
tl;dr: If doing it in excel works for you, keep doing it in excel.