Routinely I claim every penny received as "Income". This can readily be supported by deposits to my bank account (both by check and direct deposit) and by Paypal transfers.
I then look at the 1099s received and if they are not more than $100 unreconcilably "off" just use them as received. I take my total "Income" amount, subtract out the face values of my 1099s (because they are entered separately) and call the rest of it "Income for which I have received no 1099s". At the end of the day, doing this has the line 1 of my Schedule C match my total receipts.
Now it is time to deduct expenses. I use the mileage method for my vehicle, I usually take the Section 179 expense for any new equipment worth a couple hundred bucks or more, include as 'supplies' less expensive equipment and actual office supply stuff I purchased not on a shop and my cell phone since it is used almost exclusively for shop related work.
I create a category in "Other Expenses" for "Reimbursed businesses claimed as income" and that is where all the reimbursements get pulled out as a single line item. This is supported by my spreadsheet of specific reimbursements for specific jobs. I then create an "Unreimbursed business expenses" line item that is also from my spreadsheet and includes required purchases on flat fee shops, purchases I made on shops that were subsequently rejected, expenses beyond reimbursements when purchase requirements could NOT be met and stay within the reimbursement amount.
As long as 1099s are not orders of magnitude off and I don't know why, I just do not worry about it. They will NEVER perfectly match whether you are a cash or an accrual tax payer unless you began working with the company during the year and they paid you enough before the end of the year that the last check you received from them covered any and all outstanding work.
1099s SHOULD only include fees and bonuses since reimbursements are not taxable but when their accountant tells them to send out 1099s based on every cent paid to you in the calendar year they trust their accountant and get stupid. Similarly, if during the year their accounting department coded your reimbursement as a bonus or a fee by accident, they are not about to go back and change their books. If IRS audits them there will be issues with their bookkeeping and reporting as the initiator of these payments. On your end if IRS audits you, you are doing what you can to claim everything and pay taxes on what you need to.