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I would handle it like this — others may do it differently:

(1) Set up a manual Asset account using the "Other Asset" type (for example, "Bob Remodel Loan" and set the Category of the personal check you mentioned to "Bob Remodel Loan" — making it a transfer to that Asset account and creating the initial balance (showing what "Bob" owes you).

(2) When a payment comes in from "Bob," set its Category to "Bob Remodel Loan" as well, making it a transfer from the Asset account to your checking account — increasing the amount in your checking account and decreasing the amount in "Bob Remodel Loan," (showing that he now owes you less).

If you are charging interest, you will need to split the payment from "Bob" so that the interest payment has an income Category (like "Interest Earned") and the principle payment is treated as above.

If you are not familiar with transfers in Simplifi, take a look at this support article: https://support.simplifi.quicken.com/en/articles/3352152-how-do-transfers-work