When tying tzitzis with two holes (like a tzeray), do you loop all four strings through both holes or loop seven through one hole and the shamash through the second? (I believe Chabad puts seven through one hole and the shamash through the second, but there holes and customs are different.)
Here is the opinion of the Itur Sofrim who told about two holes and all the threads are in the both:
תוחבן במחט בשני נקבים בטלית ומטיב ראשיהן בתוכן ראש אחד בנקב אחד והשני בנקב אחד וכופלן והן שבעה חוטין שוין באורך ארבעה אצבעות והאחד עודף עליהן ארוך מכאן ומתחיל וקושר קשר סמוך לטלית
In Shulchan Aruch OC 11, 9, the Biur Halacha in name Peri Megadim said that the two holes must to be horizontally aligned, as the OP mentioned.
So, we see the source of two holes is the Baal Haitur, and he wrote that all the threads must be in each of the holes, the first extremity of each thread comes out of the first hole and the second extremity of each thread comes out of the second hole.
When tying tzitzis with two holes (like a tzeray), do you loop all four strings through both holes or loop seven through one hole and the shamash through the second?
--> No, the genuine Minhag of two holes is to enter all the threads together in each hole.
Poskim wrote that this minhag is a kind of chumra (to have one Talit with one hole, the Gadol one, an one with two holes, the Katan one). The two holes are for the Talith Katan only to avoid conceited behaviour. Because the holes in Talit Katan are generally not apparent (Magen Avraham in name of the Bach).
This Minhag was strongly observed in Poland (Mishna Berura). The Arizal himself maintained this minhag (imported by him from Ashkenaz Kaf hachyim), but did not try to influence Sepharadim students.
In the Shulchan Aruch of Baal Hatania, only on hole is mentioned.
The source of the Chabad Minhag is the Sidur of The Baal Hatania
אזי עצה טובה לו לעשות עוד נקב קטן סמוך לשפת הטלית שמצדה לרוחבה, למעלה מקשר גודל מהזוויות שלמטה, ולהעביר שם חוט הכורך שהוא הארוך, אחר שעשה הקשר העליון כראוי, קודם שיתחיל לכרוך.
Its purpose to ensure tzitzit hang off the side (that they go out from the lateral edge), he gives a patent to make a second little hole laterally to the first hole and to introduce in this hole the longer (which wrap the last 7 threads) thread only, in this second hole. He does not mention the Baal Haitur, and indeed, this minhag is a derivation from the minhag to make one hole, not from the minhag to make two holes. It is surprising because one can argue that this not regular no for the one hole followers and not for the two holes followers. The text of the Siddur is very short and I don't understand the reasoning. Perhaps, he think that there is no psul do make several holes. we can understand this from the words of Beth Yossef, who mention people who are stringent to make two holes, despite that he criticize them.
The second hole is out of the regular area to make a hole following Gemara reported by Itur. So, I am not sure that he is counted. From the words of the Siddur I understand that all 4 threads are in the first hole. The longer thread only is inserted in the second hole which is "not regular" for a practical reason only, not linked to the rules concerning holes. This is very congruent with the Mishna Berura who said that the two holes minhag is Polish. Chabad are not polish but Litvish and follow the Litvish minhag to make one hole only.
Note that he says this for both Tzitzit Katan and Gadol.
I believe Chabad puts seven through one hole and the shamash through the second, but there holes and customs are different.
--> Yes two differences, they make this also for Talith Gadol, and the Chabbad Minhag is not derived from the Baal Haitur, which is not mentioned at all in the SA Harav, and the purpose of the second hole is only a technical pattent to ensure tzitzit han off the side.