Thank you for attention. Problem was solved during weekend. Solution was pretty unclear for me, but it works. 1.Power down HOST Server and MD1000 2. Remove all Drives 3. Power up MD1000 4. Power down MD 1000 5. Put EMM to slot No.1 6. Put all Drives into MD1000 7. Power UP MD1000, Power up Server. 8. Now in POST Configuration Utility (Ctrl+R) we got all drives. 9. Clear PERC6/E config  10. Create VD with array of any kind 11. Initiate Initialization of created VD (Not Fast Init) 12. Power down HOST Server power down MD1000. 13. Put EMM to Slot 0. 14. Powerup MD1000 powerup HOST Server 15. Drop previously created VD 16. Create new VD  in this case RAID 10 (with 2 six disks spans) 17. Initialize it . 18. Voila.  Work done
Brand NEW Hardware Supplied by DELL (configuration was confirmed by DELL as correct)   Config Description : PE R710 with PERC6/E on-board  (PERC 6/E connected to "IN" port on EMM  , connected to MD1000  (1 EMM Module, Unified Mode, 12x750 Gb SATA drives located in drive bays from 0 to 11) Symptoms: 1. PowerUp the MD1000 2. All "Drive Carrier LED Indicators" several times blinks with green lights 3. power Up R710 4. EMM Indicator also green  5. Enclosure status LED" Flashing Amber" which means FAULT 6. During The POST the PERC 6/E Adapter Ctrl-R utility reports that no drives connected 7. Seems like New Hardware defective or incorrectly  initialized. And SYsAdmin has no chances  to understand what happens only official DELL support can help. 8. DELL's  partner already informed about this fault.
MD1000 with PERC6/E , not recognized by HOST SYSTEM