It depends on the tense but "ㄹ" is omitted in any tense.
present: 만드시다 = 만드+시다 (We don't actually use this one)
present cont.: 만드신다 = 만드+시+인다
(Many ways to express the present continuous tense but seems most simple)
eg1. 할아버지가 음식을 만드신다
Just for reference, the following is also common and natural:
eg2. 할아버지가 음식을 만들고 계신다.