Need sources of knowledge about settle

Hi All R and Shiny Enthisuasts (and the rest of you ;))
It's nice to share my first thread within this community.
I'm asking you more for knowledge sources, similar threads than solutions itself.
For now I need to challenge three below cases:

I was asked to implement basic shiny elements for some old Markdown report.
Wondering in which part should I place shiny script within a existing code or should it be placed in separate shiny module.
&
How it is possible to first run the shiny userform and pass variables (input paths) to the Markdown script, after that start knitting the report.
&
What are the steps to make project available on sharepoint

I will be very glad for each source, tip or discussion.
Adam