The Council felt that this planning charge was a tax from which it was exempt under the Protocol on Priviliges and Immunities (now Protocol 7), so they litigated. Much ado later, they're arguing before the Belgian Council of State, which now wishes to hear who gets to speak on behalf of the EU/Council.
Art. 282 EC provided the start of an answer:
In each of the Member States, the Community shall enjoy the most extensive legal capacity accorded to legal persons under their laws; it may, in particular, acquire or dispose of movable and immovable property and may be a party to legal proceedings. To this end, the Community shall be represented by the Commission.
However, in practice things aren't actually that simple. As it happens, the Commission is accustomed to let each of the Institutions litigate for itself "in matters relating to their respective operation" (cf. art. 335 TFEU). This practice is now blessed by the AG, in anticipation of art. 335 TFEU which adapts the legal rule to the habits of the institutions:
(...) the Union shall be represented by the Commission. However, the Union shall be represented by each of the institutions, by virtue of their administrative autonomy, in matters relating to their respective operation.
The next problem is whether it matters whether the Commission's decision authorising the Council to represent itself in these proceedings names a specific natural person. Is it mandatory for a natural person to be named? And what are the consequences if subsequently a different person takes over? In this case, the Commission had named the Deputy Secretary-General, De Boissieu, but much of the subsequent litigation had been carried out by the head of the legal service, Piris. The AG argues, quite reasonably, that this is an internal matter of Council administration, that does not concern the Commission or the Belgian authorities. The Council will be represented by whomever it pleases. (par. 52)
Finally, the AG suggests an interesting obiter dictum, an answer to the second question posed even though strictly speaking no answer is necessary. (Since question one was answered in the affirmative.) He argues that it is not for the courts of the Member States to sort out these kinds of delegational issues between the Institutions:
57. (...) any review of an authority granted by the Commission to the Council comes within the exclusive jurisdiction of the Community courts, for any involvement in the matter on the part of national courts would constitute an unlawful encroachment on the autonomy of the European Union institutions.
58. For which reason, even if an authority is manifestly invalid, a national court cannot do other than refer the appropriate question for a preliminary ruling under Article 267 TFEU.