I see 33, Water and Bastille Day listed on most sites for what is on disc one of BSG S1 but I also thought I remember hearing mini series was added? Was looking at getting this as gift soon and need to know if I need to order Miniseries set with this as well. thanks

yes, the miniseries is on disc 1, with the regular series starting on disc 2.
One thing to note, the extras that on the season 1 set are different from the ones in the miniseries stand-alone.

Be careful. The first season was originally released as a Best Buy exclusive box set that did not contain the miniseries and had no bonus features. The opening credits of each episode are also different (they use the UK version for S1). Later, the general release box set included the miniseries and added a bunch of bonus features (and uses the US versions of the episodes).

If you shop at Best Buy, they may still have some of the old version on the shelves.

Could you list what features from the mini-series did not make it to the S1 set?

The one I know for sure did not make it is called The Lowdown...now here is where it gets confusing. There IS a feature called The Lowdown on the box set, but it is completely different to The Lowdown on the mini-series set.
Personally, I think the uncomfortable moment between Starbuck and Starbuck at Starbucks is worth the price for the mini-series disc.

Agreed.

There's also a bunch of deleted scenes on the single disc that didn't get carried over into the box.