By 'water conditioner', I anticipate you are referring to a water softener.
Any iron removal filter should be placed before a softener otherwise, the softener will be forced to deal with iron as opposed to the iron removal filter. While a softener may be utilized to remove some iron, it is not the most efficient or effective method depending on the iron content and other water conditions. Iron will foul the resin over time unless additional maintenance is incorporated on a regular basis.
What media is currently installed in the 'whole house' filter that utilizes the mechanical Fleck 5600 control valve?
While air injection is one method to oxidize ferrous iron to a ferric state so it maybe removed by mechanical filtration, it is not the only method and is not necessarily effective for every application. The most effective method will be largely dependant on the conditions of the raw water.
Do you have a current lab test report to post? If not, National Labs offers a Well Standard test package which will be effective to assist to determine appropriate treatment recommendations.
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