We're going to be installing an HRV in our new construction.  Because we have radiant flooring, it will need it's own designated ducting on two floors.

Some questions:
- is it a bad idea to have the HRV vents in the floors of some rooms (e.g. coming up from the bottom floor) rather than running ducts through the attic (in addition to the ducts that will run across bottom floor/basement ceiling)?

- have read conflicting info that supply/return should be in same room and also that it should NOT be in same room.  If no forced air system, which is it?

- have also read conflicting info re intake/exhaust.  Some say it's ok to put close to one another.  Common sense tells me that it wouldn't make sense (why pull in air you've just exhausted?)

- if the intake if far from the unit, does that affect performance?

- suggestions on good HRVs?

where are you located?

have a look at venmar eko - hrv and erv - and regarding the install I'd go by their recommandations

adi
http://torontonetzerohouse.blogspot.com/

The Ultimate Air unit is also very efficient (both the motors and heat exchanger). 

Check out efficiency numbers of HRV/ERV untis at http://www.hvi.org/resourcelibrary/proddirectory.html