The most important factor is a uniform plant stand; both plants can compensate lower stands by tillering.
It is recommended to have majority of fertility, especially for fall rye, applied in the fall. Nitrogen top ups in winter wheat can be applied in spring based on estimated losses. Spring applications should be applied as early as possible, as both plants use majority of nitrogen early in the growing season. Fall rye uses 90-95% of total nitrogen, where as winter wheat uses between 30-40%, at stem elongation timing.
Both crops are great weed competitors, especially once established. Due to this, many times an early spring herbicide application is not necessary. Fall applications should be done to control winter annuals and perennials with a pre-burn application. Fall rye has allelopathic properties, which reduces the ability for weed seeds to germinate. An in-crop herbicide should still be applied in winter wheat for control of wild oats and spring germinating broadleaves.
A fungicide application is often not necessary in fall rye but can be beneficial in winter wheat. Winter wheat is susceptible to the same disease spectrum as spring wheat, so disease management is important. Since it is susceptible to fusarium head blight, a fungicide application should be made at head timing. Fall rye is prone to ergot. Avoiding tramping the crop, like with a spring herbicide application, can help decrease the risk for ergot.