This is an exact replica of the discussion that took place when EK put their A380 into Manchester. Arrivals, ILS interference, approach separations, etc. They work through it all and then will have the confidence to increase capacity. So, yes, you will have teething issues but eventually it all gets ironed out.
Most of these issues were resolved prior to the start of the EK A380 MAN operation, such that the first appearance of an A380 at MAN was on the first revenue service; no proving flight required for airfield procedures or ground handling.
As far as special runway procedures are concerned there are none anymore - I think there were some in the early days.
From the latest MAN aerodrome manual - ASI 11 page 194
MAG World - Aerodrome Manual
Both runways at Manchester meet ICAO Code E requirements. Paved shoulders are provided and offer protection against jet blast erosion and ingestion by the outboard engines of very large aircraft. The use of these Runways by Code F and larger aircraft is acceptable provided that the aircraft operator has certification from their respective regulatory body to operate the type from such runways. There are no specific aerodrome or ATC procedures applying to the use of runways by very large aircraft other than restrictions on the exit and entry points which may be used.