If you are on a cash basis rather than accrual then all purchases, whether resold or not, are a deductible expense.  You can bill the customer for the custom labor part and for an expense reimbursement.

What I would recommend is to set up an inventory in QuickBooks and bill it to yourself and also to your customers.  The part billed to yourself can be applied to your Chemicals Expense and the part billed to your customers can be applied to your Reimbursed Expense Income. 

When you make purchases you would expense all of it initially to an Inventory Expense account which would make it a deductible purchase whether it was sold during the year or not.  When it is used on your farm it would move via the billing from the Inventory Expense account to the Chemical Expense account.  When you sell it to your customer it would move via the billing from the Inventory Expense account to the Reimbursed Expense Income account.  The sold price can be different than the consumed price and the software will keep the totals balanced.  The profit will go to an income account.

Cost of Goods is not part of cash accounting, therefore I would not use that as a name in the General Ledger accounts.  Neither is it necessary to report inventory levels on the tax return or consider any remaining product at year end that isn't sold.  You expense all of everything you have purchased whether consumed or not.

At tax time you may wish to enter the cash purchases manually on the Schedule F, however the software can be mapped to report to the correct lines on the Schedule F. 

You don't need to keep separate records and report the custom income as a Schedule C.  You can do this just fine on the Schedule F using the methods I have outlined here.