Hi @dudeguyman Welcome to the community!
The way I handle that is to categorize the deduction as “Savings” or “Investments” …something like that, where that category is an Expense and you’re tracking that in your budget. Then, where the deposit may show up in the download from your Investment account, categorize that as an “Investment Transaction,” where the type is, “Transfer” in your Categories sheet, and “Hidden.”
This keeps a record of your transactions, but the impact is seen as a savings deduction from your budget and an increase in your investment account balance. Here is another post with that discussion.
The accounting folks will tell you that your transfers should always sum to zero, to be sure all is being kept straight. (They’re usually right! 
) Here’s another post that talks about that.
An exception to this method is a credit card payment. In this instance, because I have already categorized elsewhere the individual transactions downloaded from the credit card as they arrived, I have created a category in my Category sheet called, “Credit Card Payment.” This is marked as “Transfer” and “Hidden.” Both the checking account deductions for the payments and the deposit of the payment downloaded from the credit card account are marked with this category. There is no budget planned for this category. It is simply a place to monitor, record, but sequester the credit card transactions that are, in fact, just transfers.
Does that help?