How should I go about making cards for words that are written identically but pronounced differently?
When you spot a pair of words that are written identically but read differently,
make TSCs with those words and use furigana with × on the front
to distinguish between the readings.
For example, you can read
Make a card where on the front you have
昨日[さくじつ] on the back
if you want to train recalling one reading but not the other.
I have given examples here.
This trick works for words that share the same meaning and for words that have different meanings.
Alternatively, if two words are written the same way, pronounced differently and also mean two different things, when you make a card, you can pick a specific example sentence that will hint at the right reading.
The last option would be to make a normal card and simply recall both readings at the same time. Recalling two things at once is harder, and this will only work for pairs where the meaning is shared but pronunciations differ.