Hi,
In general migrations questions are beyond support, but few tips I can share.
Each template has its own template module positions, so after you will switch from RT to Helix - you have to change module postions to new names and if you have too small number of them, add a new ones using Helix Layout builder. In theory you can rename all module positions to keep this same names, but it depends on you.
On your place I would ... play with a Helix template on new subdomain (new.mysite.com) - where you would have installed website backup. Then you have 100% flexibility and freedoom, right.
Then AFTER you can just move whole site or just export-import settings etc..
Think smart, work less, be safe.