How to format the output of this query into year...second?
you can try Right('0'+ Cast(expression as varChar(3)), 2) like this:

SELECT Right('0' + Cast( FLOOR ( UpTime / 31207680 ) as varChar(3)), 2) + ':' -- YEARS
  + Right('0' + Cast( FLOOR( (UpTime / 2600640 ) - FLOOR ( UpTime / 31207680  )  * 12 )  as varChar(3)), 2) + ':' --  MONTHS
  + Right('0' + Cast( FLOOR( (UpTime / 604800 ) - FLOOR ( UpTime / 2600640 )  * 4.3 )  as varChar(3)), 2) + ':' --  WEEKS
  + Right('0' + Cast( FLOOR( (UpTime / 86400 ) - FLOOR( UpTime / 604800 ) * 7 )  as varChar(3)), 2) + ':' --  DAYS
  + Right('0' + Cast( FLOOR( ( UpTime / 3600 ) - FLOOR( UpTime / 86400 ) * 24 )  as varChar(3)), 2) + ':' --  HOURS
  + Right('0' + Cast( FLOOR( ( UpTime / 60 )   - FLOOR( UpTime / 3600 ) * 60 )  as varChar(3)), 2) + ':' --  MINUTES
  + Right('0' + Cast( UpTime - FLOOR( UpTime / 60 ) * 60  as varChar(3)), 2)  --  SECONDS
FROM ( 
    select @secs as Uptime
   ) AS RadheX