If you can confirm the upgrades at booking then I think using GPUs is a no brainer since like others said; they expire.
On the other hand if you can't confirm them then it makes it more difficult. Pay $1800 for a maybe and burn GPUs if confirmed, or $1000 for a maybe and fork over an extra $500 to $1000 + miles if confirmed?? I think this depends on how good you think your chances of the GPUs clearing are.
I usually use GPUs when I can confirm R space at booking. Otherwise, I typically use miles + co-pay to play the lottery.