If I assume this is mouse macrophages, then the best way is using congenic mice. I have had no problem in the past using CD45.1 mice and their CD45.2 normal controls, the specific fluorescently antibodies against these enable easy separation of donor and host cells in flow cytometry (after tissue dissociation). You could also do tissue sectioning/ immmunohistochemistry or tissue lysis/ qPCR. If you dont want to use congenics and want to label cells, this becomes more complicated, but dyes such as CFSE can be used to track cells. My worry would be that ex-vivo programming makes cells ill suited to surviving in vivo, especially if you're doing i.v. injections, these cells are not supposed to be in the blood after activation, and the adhesion molecules/ space restrictions will probably get them trapped in the lung (like metastatic tumour cells).