What's missing here, OP, are details of what is already on the 3 TB drive unit. You say it has 2 TB Free, which suggests that you are reading some info on it and it tells you that this drive has a TOTAL of 3 TB available, and that only 1 TB is used and the rest is free. Is that right? If so, then that drive is partitioned into ONE partition that covers the entire unit, and you cannot CLONE stuff from the other drive onto that space. You MUST use a set of COPY operations to place copies of all the files from the second drive into that one Partition along with whatever is there already.
Background: for any hard drive, the first thing done in preparing for storing files is to do a Partition operation. What this actually does is create a small "file" at a particular spot at the start of the drive with details of how all the space on this unit will be organized. It MAY be set to use ALL the space in one Partition, OR is may be set up to make a smaller Partition, leaving unused space. Later another operation can be done to create a second Partition (or more) in that space. The result of this latter process is that the single unit appears to be two or more separate hard drives with their own letter names. AFTER each Partition is created, a second step on that one partition is done to FORMAT it - that is, to create at its beginning the tables for data on file names, sizes and locations as they are written to this Partition. Very often now those two steps - Partition and Format - are combined into one easy step called Initializing.
Now, any CLONING operation will make a COMPLETE duplicate of the original disk onto space on a new disk, and that includes all the hidden housekeeping sections of the data tables. For this job it MUST have absolutely empty space because it cannot "work around" stuff already there. So the normal way a clone is made is to erase completely anything on that destination drive and start from "scratch". Many cloning utilities have a second option IF the drive already contains one Partition PLUS some unused space. In that case it can use ONLY the empty space not already included in the existing Partition to create a second Partition to hold the cloned copy. BUT this is possible ONLY if the destination drive does have UNUSED space of sufficient size to hold all the stuff to be placed in the clone copy.
So, IF that 3 TB unit has ONE partition on it that is much LESS that 3 TB and the rest of its space is NOT part of another Partition, then a cloning utility can do that second option of creating a second Partition on the destination drive and filling it with the cloned info. BUT if the 3TB unit has only one Partition on it that is ALL of its space, then you can NOT use a cloning utility - it WILL ERASE all the old data! In that case you MUST COPY all the files from the second drive into the empty space available in the only Partition on the destination drive.