If you wish to transit thru the Netherlands as an Iranian Citizen, you will generally need a transit visa. This is clearly stated on the Goverment.NL website and is shown in this PDF from the same as well.
There are some exceptions (Immihelp) to this rule even though the Embassy websites do not state them very clearly, one of these exceptions (Wikipedia) would be the Long Stay Type 'D' visa that you hold for Ireland.
The exception should be perfectly valid in your case and many sources verify this as well.
Note, considering the case of using the two flights (which I beleive would be on different reservations) you can obviously do it, but if your luggage is not checked in thru and thru, you will have to collect and re-check in your luggage which would require you to pass thru border control and you will need a visa in order to do so (a Proper Short Stay Schengen Visa). If you can have your luggage checked in thru, there shouldn't be much else to take care of beside the Ukraine side of things, the Netherlands should be alright.