How would you like to drink water in your earlier used utensil or washed one?
The probable answer is Yes. Similarly, intake of breath will be effective if the nostrils are cleared and clean. It is just like servicing your vehicle for good performance. So, you should do neti before pranayama. Neti not necessarily be done every day, once a week is sufficient. Because mucous layer is also essential for our nostrils for air thermoregulation before entering into the lungs and filtering the dust particles and microbes in the air.
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In rare cases, when you suffer any sort of congestion, only then you can try to do pranayama before neti, so that water can flow easily across both the nosrils in either direction.