How to change infill settings for specific sections of a model?

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Hello, all! I'm hoping one of you fine folk can help me on my 3D printing journey! I have a relatively simple piece that I'm trying to get ready to print on a Prusa MK2. I'm using Fusion 360 and Slic3r. There are two sections on the piece, on either end of it, that I would like to have 100% infill for, while leaving the rest standard. I found these three pages as I was trying to figure it out -
http://www.instructables.com/id/Change-Infill-Density-in-a-Specific-Section-on-a-3/
http://slic3r.org/blog/modifier-meshes
Both seem to address my exact issue, but for the *life* of me I can't figure out how they're doing it. When I try to sketch a box around the first section and intersect it, it gets rid of the rest of the original body outside the merged section. I tried saving/reloading in case it was a bug I'd read about (where the model vanishes but is still technically there), but it's not.
I tried saving the sketched/extruded box as a separate Object, saving it as a stand alone .stl, and importing it to Slic3r, and loading it through settings as a modifier, but nothing shows up in slic3r. It shows I've loaded it in the file list, but I don't/can't see it on the print bed display.
Those two sites are helpful but there's some key component I'm missing here and I've spent hours trying to crack it. I'm sure it'll end up being something relatively straight forward but I'm hoping for a nudge in the right direction.
Thanks much in advance!!