For the snes9x? I managed to figure out how it works after messing with it. I'm definitely not an expert on this, but I will do my best to help you out.
The lover digits past 09 cannot be entered as the values listed here. You're not allowed to input them as such because the new value section seems to only accept numbers, not letters. 0a is 10, 0b is 11, 0c is 12, 0d is 13, 0e is 14, and 0f is 15. Those numbers afterwards (10-18) are shifted up to 16-24. I'm going to use Levin and Tiltyu as an example. Levin's code is 08, as it is listed, but Tiltyu's lover code must be input as 21, because 15 is really 0f (Dew).
So the full code would be Levin's lover modifier code with Tiltyu's lover digits for Levin and Tiltyu's lover modifier code with Levin's lover digits.
7e2aac21 for Levin and 7e2a1c08 for Tiltyu.
In order to get started, go to cheats, then click on 'Search for New Cheats(active)'. A small window that looks like this should come up:
From here you have two options. You can search through the cheats manually to find the code you're looking for, but that's really tedious. I recommend performing a search for the code by doing the following:
Under the 'Comparison Type' section, change the selected comparison type to =(equal to). Under the 'Compare To' section, change it to entered address. It should look exactly like the picture I provided above. In the search bar where it says Enter a Value, enter in the code you're trying to find. For example, you'd enter Levin's lover code modifier (without the xx at the end). I did so in the image above as well. After you enter the code in the search bar, click the search button. The address should come up. The goal here is to change the current value of the cheat to the lover digit of the person you want Levin to be in love with. Click on it and it should be highlighted. The add cheat button below the search button will become clickable. Click on it. Put the lover code in the new value section. It should look like this:
Click ok
In my example, Levin was already in love with Tiltyu so I changed the digit to 15 just to demonstrate the process.
Note: The fortune teller does not seem to acknowledge lovers obtained this way. When I had Levin paired with Dew, it said he didn't have feelings for anyone. I tried it with Aideen too, and the result was the same. For all intents and purposes, both Dew and Aideen acted as Levin's lover. Levin could use the give command and had the lover bonus when standing within 3 spaces of them.
Levin could even get lover criticals from them even though Aideen and Dew were not in love with Levin and had other lovers:
Now to change it back to 21...
Tiltyu is his lover again. Now you have to do the same for Tiltyu. Make sure to click the reset button before you search for another code. Search for Tiltyu's lover modifier code, 7e2a1c. Put 08 (Levin's lover digit) in the new value section, click Ok. Now they should both be in love with each other.
If you pair a mother with someone this way, the game will still register them as being paired even though the fortune teller doesn't say they're bound to each other. Don't let that bother you; you'll get the children as you would if you had paired the parents normally. In case anyone is curious, pairing two mothers with each other yields two sets of subs. xP
I hope this helps... Sorry if it's confusing.
EDIT: Oh, I figured out why it doesn't accept letters. If you want to use the lover digits as they are listed in the guide, you have to change the data type (it's right under the compare to section) to hexadecimal.