Quoted: From what i've read I should sight in at 50 yds to zero,  make it good out to about 300 yds?

A 50y zero will also zero at 200M (about 218yards), out to 225y or so the bullet will be +/- 2.5" from the point of aim.  At 300y you're going to be hitting about 6" low.

I have a flip up sight with two appatures no elevation ajustment on it.  just windage.  Should I use small or big hole to sight in

Small hole generally.  Only zero with the large hole IF your apertures are offset from each other AND you only intend on using the large aperture.

and what diference will switching between the two make?

We have no way of knowing as you didn't tell us your rear sight model.

Some models (like the Troy) are 'same plane', so you can use either aperture and they will hit the same point.

Other models may use the A2 aperture, which generally means you're going to be hitting low compared to the small aperture.  Since there are at least 3 different variations in the offset you're going to have to go to the range and shoot your rifle to find out.

Quoted: Where should I zero to be accurate out to 300-350?

Honestly there is no zero with the .223 round that will give you a flat trajectory for muzzle to 350.  

If you limit your expectations to 300y.  Then your best option will be the 50y zero.  Minute of beer can to 250y or so - and only a 6" drop (2moa) at 300y.

If you want to shoot beyond that I'd suggest getting an elevation adjustable rear sight (like the LMT or KAC 600M) then you can dial in the range.