TN-1 was specifically designed for this sort of situation, so if you have TN-1 and continue to qualify for it your immigration situation is fine, nothing makes them happier than telling them you still live in Canada. TN-1 only becomes dicey when people try and stay in the US for very long periods of time.
For details on the tax situation read:
http://www.cra-arc.gc.ca/E/pub/tg/p151/README.html and IRS publication 519.
To wittle it down for you, don't worry about the substantial presence test, clearly you are resident in Canada for tax purposes.
If you have to fill in a W-4, have a read of page 24-25 of IRS publication 515 which tells you how to fill it in as a non-resident alien.
Basically, they give you a W-2 (if you're paid in the US), you fill in a 1040NR and a Form 8840 to declare your income every year and send it in at tax time. If you've paid US payroll taxes, you claim a foreign tax credit in Canada for them. The general guide for the T1 explains how to do this.
If they still pay you in Canada then you get a T4 anyway so nothing changes essentially, although technically you are still supposed to declare your income to the US and pay US taxes on it at tax time, claim a foreign tax credit, etc. if your US-source income exceeded $10,000 or you were physically there for more than 90 days. However I doubt anyone does if they get a T4, but you're supposed to. Either way you still pay the same amount of tax, just to different countries.
If you've got TN-1 already, I'd suggest going down to the local SSA office and applying for an SSN, it will speed things up if they want to give you a W-2 (i.e. you're on the US payroll).
Steve.