Depends on what the order is. For combat related orders, the answer would be no. An SS officer couldn't show up and just say "alright, get your guns were going to attack that hill." The Wehrmacht officer would have control over the military matters. Obviously this varied though, and an SS man could be put in charge of an army formation, and in that case the Wehrmacht soldiers would have to listen. An example would be Heinrich Himmler, who briefly found himself in charge of several army formations despite never joining the Wehrmacht.

However, the army seceded control over undesirables and so called "partisans" to the SS. For example during the invasion of Poland the Wehrmacht allowed SS and Gestapo free reign to deal with subversive elements like Jews, Polish intelligentsia, etc. Same would go for Barbarossa. So if an SS officer showed up and ordered Wehrmacht soldiers to turn over say...all Jewish partisans for execution, the Wehrmacht soldiers would be expected to comply. A good example is the Einsatzgruppen, they would have used army resources and cooperated with the army, but were under strict SS control and acted independently of the army.

I think the definition of Wehrmacht is a start, the Wehrmacht was the "German Armed forces" i.e. the Army (Heer) Navy (Kreigsmarine) Airforce (Luftwaffe). The Waffen SS was NOT part of the Wehrmacht but was placed under the operational control of the army during conflict. So with that definition in place, lets move on to part II. The SS had two separate rank structures. There were Allgemeine SS ranks(the general SS for all intents) and then there were Waffen SS(armed SS) commanders like Sepp Dietrich and Paul Hausser who held the equivalence of Colonel-General rank (Oberst-Gruppenfuhrer). They both commanded field armies which had significant amounts of army troops. In Paul Haussers case, he was an SS General who commanded army group G, of which the majority of its battle order were Heer. Sepp Dietrich on the other hand commanded the 6th SS Panzer Armee which had 3 SS Panzer divisions and a couple of army divisions thrown in. So yes, it was entirely possible to command Heer Soldiers in the field. HOWEVER, SS Colonel such and such from Berlin would likely not show up on station in the middle of Krakow and take command of a Heer or even a Waffen SS formation. The German military was pretty formalized and functioned in that manner, i.e. you were not placed in command unless you had the necessary pre requisite of training to do such. In the EXTREME RARE situation such as Himmler commanding Army Group Vistula, Hitler believed he would inspire (with fear I guess) the troops to hold the line. Himmler proved grossly incompetent as a commander and was relieved after several weeks.