Yes. Or course. You will need to manually assign devices however if products in a single product category must be assigned to both instances. For example, you purchase two new Macs and one needs to be in MDM 1 and the other in MDM 2. If you are allowing automated assignment based on product category "Mac," then both devices get assigned to whatever the default MDM is. In the short term, you will need to spend more time in ABM getting device assignment correct.
Also, you will need to create a new location so you can get a second VPP token. Do NOT attempt to use one VPP token on two MDMs.
If this is a merger, you will likely want to setup the long road of retirement through attrition. Set all new devices to go to your "forever" MDM and then allow the ones in the "to be retire" MDM to simple age out. Or migrate as people turn over.
Hope this helps