The USCIS recently answered this question in a FAQ memo on H-1B filings.
USCIS recomments that petitioners clearly label all H-1B cap cases in red ink on the top margin of Form I-129. Use the following codes:
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Regular Cap (65,000 regular cap cases, not including Chile/Singapore cap cases)
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C/S Cap (Chile/Singapore H-1B1s)
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U.S.Masters (20,000 cap for beneficiaries with U.S. Masters or higher degrees)
A separate check for each applicable filing fee (Form I-129, Premium Processing, Fraud Fee, and/or ACWIA fee) is preferred. Applicable fees should be stapled to the bottom right corner of the top document.
This is the USCIS preferred order of documents at time of submission.
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Form I-907 (if filing for Premium Processing Service);
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Form G-28 (if represented by attorney or accredited representative);
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Form I-129 (“Petition for a Nonimmigrant Worker”);
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H Classification Supplement to Form I-129;
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H-1B Data Collection and Filing Fee Exemption Supplement;
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Provide a Table of Contents for supporting documentation:
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Tab items as listed in Table of Contents;
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Arrival-Departure Record (Form I-94) (if the beneficiary is in the US);
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If applicable, the SEVIS Form I-20 (if current or former F‑1 student or F‑2 dependent), SEVIS Form DS-2019 (if current or former J-1 or J-2) or Form I-566 (if current A or G nonimmigrant)
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Certified Labor Condition Application, Form ETA 9035, from Department of Labor;
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Employer/Attorney/Representative letter(s); and
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Other supporting documentation.
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Duplicate copy of the petition if the beneficiary will be seeking nonimmigrant visa issuance abroad. Clearly identify the duplicate copy of the petition as a COPY, so that is not mistaken for a duplicate filing.
To read the entire USCIS FAQ on this subject, please click here.