There shouldn't be a lot of difference, other than flavour. You may find it better going for a cooking style apple like a Bramley - the filling will then develop a smooth texture. With eating apples, the apple pieces keep their shape..
Are you adding water as part of the recipe- it may be that you have a added a little too much - the apples will let out a fair amount of juice anyway, adding water will make teh dish more runny.
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