I've found that for me the side-effects stayed the same with increased dose, but the expected effects kicked in suddenly as I passed a 'threshold' dose. (not sure if he explained to you how to increase your dose; some consultants like to do this under supervision and others suggest you do it yourself, but don't fiddle if he didn't tell you to!)
You do need to keep at it for it to work properly as part of it is about getting into a new routine - this also means getting up at the right time each day and making sure you eat at regular intervals. I get up at 7-8 every day (having had the amitrip at 8 the previous night), have breakfast, lunch at around noon, dinner at 7:30 and bed at 10 - even quite small deviations from this cause me massive swings in pain/fatigue/concentration, but some of this will be autonomic stuff. Once you've got yourself into a pattern you can start to experiment a bit more
I also set myself an alarm on my phone to remind me to take my pills - otherwise I usually forget.
If you think it will be a problem getting up then I would say it can't hurt to tell work - but it depends how nice they are. If I rolled in at 11 my boss wouldn't bat an eyelid but yours might
In theory they can't hold it against you if it's a medical thing but obviously this varies, especially with small firms.
Hope it helps you, anyway