This question must have been going round since the earliest days of the Net and still, there is no definitive answer!
We know that the famous 1798 uniform, portrayed in the set of plates published by Mollo, was actually promulgated on 1st January 1799 and that the 1798 black-lacquered musket was only completely introduced ten years later! We know the Austrians had a few thousand kasketts in the Mantua stores shortly before and that the officers would have bought their own uniforms in the new style, while the men had to wait for the issued kit.
The real problem is the sources, as the original issue records do not appear to have survived. The Mollo plates are very well known as are Seele's paintings, which are usually said to show the army in Switzerland in 1799 with the uniforms in transition. In fact, the latter were painted around 1805 in Munich, but maybe the sketches were drawn when the Austrian army was in southern Germany in 1799/1800? The "real" 1799 set mentioned above are here http://www.uniformen.napoleon-online.de/index.php?/category/77 but unfortunately, do not show the main infantry uniform. It does however show the Strozzi light infantry (1st light Infantry battalion) still in the old Freikorps unform.
The new uniforms and kit would have gone to Germany/Switzerland first, so the presumption has to be that the army in Italy would have still been in old uniforms with its officers mostly in new uniforms. That is not certain!