A domino is a $1\times2$ or $2\times 1$ rectangle. Diego wants to completely cover a $6\times 6$ board using $18$ dominoes. Determine the smallest positive integer $k$ for which Diego can place $k$ dominoes on the board (without overlapping) such that what remains of the board can be covered uniquely using the remaining dominoes.
1. **Understanding the Problem:**
   - We need to cover a $6 \times 6$ board using $18$ dominoes.
   - Each domino is a $1 \times 2$ or $2 \times 1$ rectangle.
   - We need to find the smallest positive integer $k$ such that placing $k$ dominoes on the board leaves a unique way to cover the remaining part of the board with the remaining dominoes.

2. **Initial Considerations:**
   - A $6 \times 6$ board has $36$ squares.
   - Each domino covers $2$ squares, so $18$ dominoes are needed to cover the entire board.
   - We need to ensure that the remaining part of the board after placing $k$ dominoes can be uniquely covered by the remaining $18 - k$ dominoes.

3. **Avoiding $2 \times 2$ Empty Squares:**
   - If any $2 \times 2$ empty square is left, it can be covered in multiple ways, which violates the uniqueness condition.
   - Therefore, the remaining part of the board should not include any $2 \times 2$ empty squares.

4. **Dividing the Board into $2 \times 2$ Squares:**
   - The $6 \times 6$ board can be divided into $9$ non-overlapping $2 \times 2$ squares.
   - To avoid leaving any $2 \times 2$ empty square, we need to ensure that the placement of $k$ dominoes does not leave any such square.

5. **Calculating the Minimum $k$:**
   - If we place $k$ dominoes, we cover $2k$ squares.
   - The remaining part of the board has $36 - 2k$ squares.
   - To ensure a unique covering of the remaining part, we need to avoid leaving any $2 \times 2$ empty square.

6. **Constructing for $k = 5$:**
   - For $k = 5$, we place $5$ dominoes, covering $10$ squares.
   - The remaining part of the board has $36 - 10 = 26$ squares.
   - We need to check if the remaining $26$ squares can be uniquely covered by $13$ dominoes.

7. **Placing Dominoes:**
   - We can place $5$ dominoes in such a way that the remaining part of the board does not include any $2 \times 2$ empty square.
   - For example, place the $5$ dominoes in the intersections of the $2 \times 2$ squares.

8. **Verification:**
   - By placing $5$ dominoes strategically, we can ensure that the remaining $26$ squares can be uniquely covered by $13$ dominoes.
   - This can be verified by trying different placements and ensuring no $2 \times 2$ empty square is left.

Conclusion:
The smallest positive integer $k$ for which Diego can place $k$ dominoes on the board such that the remaining part can be uniquely covered by the remaining dominoes is $k = 5$.

The final answer is $\boxed{5}$.