Assuming you are using the most recent version of Mesen, and you have already tried using the HD Pack Builder feature (but aren't sure where your sprite/tile is located in the pack) - you can follow the process below:
-Start the game and play until you reach the area you want to edit.
-Navigate to Tools.
-Select Tools Within Debugger.
-Select PPU Viewer.
-Move your cursor over the area you are trying to edit.
-Select "Copy Tile (HD Pack Format)"
-Now, navigate to the HD Pack you are working on and find the file within called "hires.txt."
-Make sure your cursor is at the top of the file and hit ctrl + F (also make sure the direction of searching is "down" if your cursor is at the top).
-Under "Find What" right click and hit "paste."
-Pasting should fill the "Find What" section with the address information of the tile/sprite you are trying to locate. It should look something like, "124,22291A0F" (I looked for the sky in Super Mario Bros + Duck Hunt and it may be different from the normal Super Mario Bros. without Duck Hunt).
-If you are lucky, it should find a match.
-If a match is found, look at the very top of the grouping of code - you should see something that is called something along the lines of #Chr_01_3.png." Take note of this.
-Also, take note of the two numbers after the the address information. You will need this later. For example, if your format looks similar to the code below, take note of the 32 and 16 numbers. These numbers represent the x and y locations of where your sprite/tile is located in the .png file.
-Now, look in the HD Pack you are working on and find the .png file that matches the tile you referenced in the previous step. Use the x and y information to hone in on your sprite/tile. Try coloring in something in this area (even if it is blank).
-Hit "Save" and test to see if it changed the area you are trying to edit.
Here's hoping this helps.