Troubleshooting these situations can be tricky, particuarly if processes are running based on business need - without the proper capacity planning exercise.

1) What does the daily upload include, can this be done in batches and at a time of low activity?

2) Have you confirmed all the Auto Create Statistics and Update statistics are enabled?

3)If so , track dow the highest impact queries Place every query in the SSMS and analyse the execution plan. First – check for tables or index scans. If large table \ index scans are occurring – progress with Query Analysis. The Query Analysis should ask questions such as : Are all JOINS valid ? Are the JOINS returning excessive data ? Search argument validity? Functions in predicate?

4) If in Step 3 you identified queries with high CPU usage , analyse in SSMS for Hash Joins, Sorts, Filters. If any of these exists , progress with Query Analysis.