Yes, the ProgIds are compatible - your duplicate matching will still work. They're actually generated by Myth from the title/subtitle/season/episode I believe. There may be the odd hiccup because I think the RT grabber used to clean up some title/subtitles ("fix-ups") whereas the Atlas one will not but generally you shouldn't notice any difference, other than getting data for every TV channel & radio too.
You cannot use apt-get yet as there is no xmltv repository that I am aware of. I have no idea when the new xmltv will get into the distribution ones. If you can wait then this is obviously the easiest way.
Otherwise, you'll already have a xmltv package installed (0.5.63-2?) but Atlas needs 0.5.64 so the only way currently to use it is;
1. Uninstall your existing xmltv packages (xmltv, xmltv-gui, xmltv-util, libxmltv-perl)
2. Download 0.5.65 and make as per the README. It's quite simple, although you may need to satisfy some other minor dependencies along the way.
3. To use Atlas you need to get a (free) key from metabroadcast, which the grabber requires as part of its configuration. This a real pain because their website/API is a nightmare IMHO. And you can only log in from a Twitter, Google or Facebook account.
It's done from http://metabroadcast.com/blog/create-and-manage-your-atlas-api-key
. And as the grabber INSTALL (https://github.com/honir/tv_grab_uk_atlas/blob/master/INSTALL
"Remember to request Press Association (PA) as the content provider on your Atlas API key."
Once you've got the magic key, you never need to go near it again (I hope!). One day I suspect the RT feed will break/be turned off/become too expensive to maintain, so better you migrate at a time of your choosing than theirs...