The Rishonim count as one of the 613 mitzvos the commandment to build a Mishkan, but do not count as separate mitzvos the commandments to make a shulchan, menorah, etc. The Rambam (Sefer haMitzvos 33) writes that these kelim are just component parts of the larger mitzvah of building the Mishkan. While it may seem strange to view kelim as subsumed under the mitzvah of making a Mikdash considering that the Mikdash can still be functional even if kelim are missing - the gemara says that even if there is no mizbayach one can still offer korbanos at its location – it is perhaps no different than a mitzvah like tzitzis, which should ideally have strings of white and strings of techeilis, but can be fulfilled even if one component part is missing. The Ramban agrees in principle that the kelim are not counted as independent mitzvos, but disagrees with the Rambam’s reasoning. According to the Ramban, the command to make a menorah is subsumed under the mitzvah to light a menorah – it is a necessary hechsher mitzvah. Similarly, the command to make a mizbayach is a hechsher mitzvah to fulfill the mitzvah of korbanos, and the shulchan necessary to fulfill the mitzvah of making lechem hapanim, etc.
The upshot of the difference in reasoning between Rambam and Ramban is whether to count making the aron as a seperate mitzvah. According to the Rambam, the aron is just one of the subsections of the Mikdash subsumed in the command to build it (see the Minchas Chinuch and Megilas Esther on mitzvah #33 why the Rambam seems to omit entirely any discussion of the halachos of making an aron). According to the Ramban, the kelim are subsumed in the mitzvos of avodah that apply to them, be it lighting a menorah, offering korbanos, etc. Since no avodah is performed with the aron, it is counted according to Ramban as an independent mitzvah. This machlokes has many ramifications… maybe more next week bli neder.