A friend of ours has recently been to see the accountant about change of tax residency from the U.K. to Spain; which any Ryanair pilot based in Spain ought to do as well. They were told that they will not be liable to pay further tax and social security in Spain if the amount of tax and NI they pay in U.K. exceeds what they would be liable for in Spain.
Assuming this is the precedent, your Ltd company pays employer social security and you pay tax and social security in Ireland. You would then need to see your Spanish accountant to ensure that your tax and social security contributions satisfy Spain's requirements.
It's worth noting that there is a bilateral agreement between Ireland and Spain for both tax and social security so you don't double pay either.
This whole Ltd contract carry on is very messy. Truth is no one on this forum really knows the answer as its so complicated. If you want to make Ryanair work longterm you really need to get yourself on to a direct contract with Ryanair ASAP from what I can see, although even then, if based in Spain, you would still need an accountant in Spain to register your tax residency and returns.