Manga cameos should be as follows depending on where HGSS is in the timeline
If its the same as GSC then,
Ruby should be fought in goldenrod (he'll be in one of the houses that had no doors in GSC)
Sapphire would be there too but you won't fight her
Blue and Red would stay in there old positions but you should be able to have rematches with Blue whenever you want. (note: I am using the US names)
Green would be fought at the Power Plant, Seafoam Islands, and Indigo Plateau (or Mt. Ember if the Sevii Islands are included) After you beat her in one place she goes to the next place sort of like the tv reporters in RSE (forgot there names)
If they expand the plot a bit further Yellow can pair up with you in Viridian Forest.
Crystal is in Earls Pokemon Academy in Violet
Now if the timeline is after DPPt,
Red, Blue, Green, will stay the same
You battle Sapphire this time
You compete against Ruby in a contest
You compete against Yellow in the Bug catching Contest
Emerald tags with you in the Battle Tower
Crystal is in Kanto as Prof. Oaks Assistant
Dia and Platina are in the top floor of the Pokemon Center when you're linking with someone playing DPPt
Oh and Pearl's dad might be in there somewhere, never got past Ruby and Sapphire volume 16 in the actual manga so I wouldn't know