Hi Phoinix
I must admit that I have no experience of flow visualisation with full-scale helicopters.
There have been tests done with smoke generators suspended above the hovering helicopter. The smoke is then drawn through the rotor and 'should' make the wake visible. You're right about the type of smoke, or flow seeding, used (One thing you wont have to worry about is it filling up a closed return tunnel!). That may be trial and error.
Thinking more about it, you could try asking the folks at Boscombe Down (QinetiQ) as they have conducted tests similar to this , I believe.
I would definately suggest posting this in the Flight Testing Forum too, there's a good chance that would lead you to folk who've actually done this.
Steve