OK if it's a cash upgrade then I think you should be able to credit to either program but I haven't specifically looked into it before.
AA's chart at http://www.aa.com/i18n/AAdvantage/ea...a-airlines.jsp says that U (which is what the upgrade would be) will be 100% EQM and 100% EQP if you fly this year or 50% EQP if you fly next year (which as a side note seem to mean that getting upgraded from Y to U gives you fewer points?)
AS gives 100% miles for U class on the chart at https://www.alaskaair.com/content/mi...on-alaska.aspx

So sounds like basically you should pick which miles you want.