There's a lot of options for intercoolers. Did you get a setup specifically designed for hot-air engines? Is it just the intercooler or is a kit that includes a new turbo housing and intake adapter? Saying what, exactly, you're working with always helps (including pictures).
The hot-air turbo feeds directly into the intake. Installing an intercooler will involve repositioning the turbo with a different outlet flange and some method for getting everything routed back to the intake inlet which is very much obscured by the turbo.