Yes, multiple lines of accounting are allowed per CLIN with multiple subline items for the appropriate ACRNs to be charged.  FAR 4.1004(a)(1)(ii)

FAR 32.206(d) provides additional specifics that need to be included in the contract:

Instructions for multiple appropriations. If contract financing is to be computed for the contract as a whole, and if there is more than one appropriation account (or subaccount) funding payments under the contract, the contracting officer shall include, in the contract, instructions for distribution of financing payments to the respective funds accounts. Distribution instructions and contract liquidation instructions must be mutually consistent.

Alternatively, if the amount to be paid and the associated ACRNs are too complex for a short description, the information could be placed into an exhibit that is referred to in the CLIN description.  This can create a cleaner look to the CLIN listing.  Reference DFARS PGI 204.7105 Contract exhibits and attachments for the procedures for creating and numbering an exhibit.