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I am planning/hoping to start a Red Scorpion army soon but I had a few questions about them first.

1) Do they use normal chapter markings for squads? The arrow for tactical squads? Upside down V for devestator? Etc...

2) How do they do company markings?

From what I see in IA 9 dealing with the Badab War, the Red Scorpions are strict codex astartes adherents as they view it as Holy Scripture.
That being said from the pictures in the book it shows tactical marines with the chevron marking instead of the up pointing arrow.



http://warhammer40k.wikia.com/wiki/Red_Scorpions

Company markings: Look at the left knee in the picture.

I think the OP is meaning the designation for what type of squad, not the squad number.