Device drivers (with the help of code provided by the kernel) can be written to use PnP methods to set the bus-resources in the hardware but only for the device that they control. But many device drivers just accept what the BIOS or Linux has configured and use code provided by the kernel to find out how this device has been configured. Since the driver has checked the configuration and possibly reconfigured it, it obviously knows the configuration and there is no need for you to tell it this info. This is obviously the easiest way to do it since you don't have to do anything if the driver does it all.
If you have old pre-PnP ISA hardware, the Linux PnP software may not know about it and the bus-resources it requires. So it might erroneously allocate the resources that this old hardware needs to some other device. The result is a resource conflict but there's a way to try to avoid it. You can reserve the resources that the old ISA card needs by configuring the BIOS at boot-time (usually), the isa-pnp module or to the kernel (if the PnP is built into the kernel). For example, to reserve irq 5 give this argument to the isa-pnp module (or to the kernel): isapnp_reserve_irq=5. See BootPrompt-HOWTO. Instead of ..._irq there are also _io, _dma, and _mem.
For PCI devices, most drivers will configure PnP. Unfortunately, a driver could grab bus-resources that are needed by other devices (but not yet allocated to them by the kernel). Thus a more sophisticated PnP Linux kernel would be better, where the kernel did the allocation after all requests were in. See How Linux Does PnP.