I would note that GEL cells really are not used much on boats these days and AGM's are the preferred type of "no maintenance" batteries.
While I would agree that wet cells are the most economical solution long term if you are NOT living aboard and at anchor much of the time....decent AGM's are actually more economical long term if you ARE living aboard for several reasons:
1. # of life cycles of recharging is several times greater than wet cells
2 the SPEED of recharging since you you can recharge at 100% of capacity rather tha 20% of capacity saves $$ in diesel since you can recharge fully in far less time.
As to the original question...many times a separate battery for the windlass is wired in to avoid long runs of necessarilly VERY thick and expensive power cables from far away. Consider this before you change your set up arrangements.
As to adding a separate engine start battery, there is no problem with that if you just add in another Perko switch (1-2-both-off).
Do NOT mix battery types...go all AGM if you are a full time cruiser or all wet cell if you are not (and don't need the maintenance free aspects). You may vary battery capacities as long as the type doesn't change.