i can add my two cents here.
first of all, i'd advise against ANY tampering with passports. it's not a good practice unless you have no other options.
i have a permanent resident HKID card which entitles anyone to use the Macau e-channel. Macau Immig would like holders of PRHKIDs to use this feature--they don't want you standing in line behind a mainland tour group. entry/exit to the MSAR is as fast/easy/painless as the e-channel in Hong Kong.
here's the easiest way to do it: get off the jetfoil and follow the crowds to Chegadas (Arrivals). before you get to the passport-lines, in the same hall, look to your left. you'll see a dull white plywood construction, possibly with some people queueing up. if you can't find it, ask an Immig employee. do NOT go thru Immig.
join the queue, and you'll see people going through curtains--beyond those is a glass-fronted desk with Immig officials behind. this is where u get permanent access to the e-channel.
you sit down and fill out a form, certifying a bunch of stuff (most important: that you won't work in Macau). they take thumbprints and a picture. then someone leads you to the e-channel. it's not like HK where you slide yr ID card into a slot--u put it face down on a small sheet of glass where a blast of light takes an image. then you retrieve your ID and go in the gate. you press your thumb as usual, but note that you must take the "arrival card" which is a little sheet of paper automatically generated, it looks like a fast-food receipt. once you take it, the gate opens, and you're in Macau. printed on the paper is your final departure date (one year in the future) and the warning that you can't work in Macau. that's it.
it takes less than a minute, and means people registered for this scheme can travel btwn HK/Macau with their ID card, no passport needed. it's also very handy at the Macau/Zhuhai border-crossing.
i don't know anything about frequent-flyer shortcuts, i'd call the air-carrier if you want to try that.
as for travel with the SO, well, you should probably bring your passports and queue up--if she knows you can enter/exit Macau without a passport-stamp, and if that's important to you, plan accordingly. i don't know if the Immig officer wd mention that you can use the e-channel when he/she stamps your passport. my guess is no, but i can't be sure. i don't use my passport to enter Macau any longer. as with any 141-related info that slips out, best to just nod and smile and not make a fuss.
the Macau e-channel is superb. doing the HK/Macau trip with e-channels on both ends makes Immig a guaranteed 60-second pit-stop on entry/exit. and when going to Zhuhai, you pass by the entire passport-visitor line and go through special lanes for HKID perm res holders only. still have to queue up for China-entry with yr passport, but that's not gonna change.
this article:
http://www.thestandard.com.hk/ne ... 6847&con_type=1
has more info, but note that it takes five working days to process the application in Hong Kong. on arrival in Macau, you can do it on the spot and use it immediately after. even if you queue for 15 minutes at the white shed, you're already saving time on a single visit...
JtB