As the title states, this manual describes the syntax of the input. The reader should not expect to learn how to model systems from this text; it is rather a reference manual where the user can find the exact and detailed description of the syntax of some entity, where it is assumed that the user already knows that entity exactly does what is required to model that system or solve that problem.
To get on the right track, one may have a look at the Frequently Asked Questions (Appendix E), a steadily growing chapter that collects the most common issues arising from users. They might help pointing to the right statement for a given purpose, but in any case nothing can replace the judgment of the user about what entity exactly fits some need. The only document that may help users in growing this type of judgment is the tutorials book, available from the website. For more specific questions, one should try the mbdyn-users@mbdyn.org mailing list (browse the archives, just in case, then post a question; posting is restricted to subscribers; subscription is free).