Like the 22RE, the 22RTE uses passages cast into the head and stock exhaust manifold to bring EGR gases from the exhaust side back to the intake side. They will work just fine with a non-stock turbo, as long as the stock exhaust manifold is used.

If you're also using a non-stock manifold, well, I'm not aware of any aftermarket turbo exhaust manifold for this engine that uses EGR passages. But if you're just using the stock manifold with either elongated bolt holes for the turbo mount or an adapter, the stock EGR should work fine.

If you're not sure what you have, post some pics and we'll point out the relevant parts.

-Jeff