I'm glad that the search is working for you.
You are correct that the typing order will change automatically, depending upon what you are typing. If what you are typing is actually a Hebrew character, then the Command Lines knows to keep the order right-to-left. But if you type something that is not a Hebrew character, then the order changes to left-to-right.
This is useful in many ways. You do not have to change the typing direction, since the Command Line already does it for you. And when you enter morphology codes, once you add the @ sign the Command Line shifts automatically to enter the codes in left-to-right order.
After you type a Hebrew word, the cursor is at the left side of the word. To add morphology codes you move the cursor to the right side of the word, then enter the @ sign. Then you can enter the desired morphology codes.
When you search on a phrase in Hebrew, the words should be entered in right-to-left order. For example, if you wanted to search on the exact phrase of the first words in Genesis 1:1 (using the WTT), you would enter, from right-to-left, the following characters:
'~yhla arb tyvarb
To run the same phrase search on the WTM, with the @ sign and and asterisk, you would use the following search. Notice the order of the characters. The Hebrew letters are right-to-left, while the @* is left-to-right, and is to the right of the Hebrew word.
'~yhla@* arb@* tyvar@* b@*