Hi Patience,
When in this situation it helps to sit down with a piece of paper and think through the pattern. As you do this jot down the finished measurements, to start. Then remember to add in the seam allowances for each piece for cutting measurements.
So for this pattern, if the large HST are a finished 5 inch block, they started as being 5 1/2 inch square....right? 5 plus 1/4 plus 1/4 for the seam on each side.
Ok, for your pattern the smaller HST blocks are three sections to the one large section. For having easy math, I would change the large HST to being 6 inches finished, with the three smaller blocks being a finished 2 inch square. You would add the 1/4 inch seam allowance, being mindful that you have seam on each side.
So the large blocks would start with 6 1/2 inch squares, and the smaller would be 2 1/2 inch squares.
Whenever you have this situation it is advisable to make up at least one block and it's sections to make sure that your calculations are correct before cutting out all of the fabric for the project. Once you have your practice block made I always have it right above my sewing machine. That way I can look up to check myself as I'm working on each block and section.
This is where a design wall is very helpful. You can take a simple cheap plastic tablecloth, flannel, or extra piece of batting and pin to the wall with poster pins. There are various other methods of having a design wall depending on your situation and space.
Good luck with your project and please keep us posted on your progress, with pictures if possible.
Pam M