How can I replace circuit breakers with GFCI breakers when it is a multiwire branch circuit?
You'll need a double-pole GFCI breaker, wired like so:


What you have described is a multiwire branch circuit. Because the neutral is shared, the overcurrent protection device(s) (in your case the two separate breakers) must be able to trip together.

This can be remedied by installing a double-pole breaker, or by handle-tying two individual breakers. However, since you already have a need for GFCI protection, go ahead and install a double pole GFCI breaker.

However, existing lights might not need GFCI protection if they are 5 ft or more away from the pool (horizontally) and 5 ft or more above the maximum water level of the pool. Within 5 ft and below 5 ft above the maximum water level is not allowed. See (B)(3) and (4).

If you move or install new lights, they are subject to new installation requirements. See (B)(1).


  2014 NEC
  
  680.22 Lighting, Receptacles, and Equipment.
  
  (B) Luminaires, Lighting Outlets, and Ceiling-Suspended
  (Paddle) Fans.
  
  (1) New Outdoor Installation Clearances. In outdoor pool areas,
  luminaires, lighting outlets, and ceiling-suspended (paddle) fans
  installed above the pool or the area extending
  1.5 m (5 ft) horizontally from the inside walls of the pool shall be installed at a height not less than 3.7 m (12 ft) above the maximum
  water level of the pool.
  
  (3) Existing Installations. Existing luminaires and lighting outlets
  located less than 1.5 m (5 ft) measured horizontally from the inside
  walls of a pool shall be not less than 1.5 m (5 ft) above the surface
  of the maximum water level, shall be rigidly attached to the existing
  structure, and shall be protected by a ground-fault circuit
  interrupter. 
  
  (4) GFCI Protection in Adjacent Areas. Luminaries, lighting outlets, and ceiling -suspended (paddle) fans installed in the area extending between 1.5 m (5 ft) and 3.0 m (10 ft) horizontally
  from the inside walls of a pool shall be protected by a ground-fault
  circuit interrupter unless installed not less than 1.5 m (5 ft) above
  the maximum water level and rigidly attached to the structure adjacent
  to or enclosing the pool.