I really need help picking out a thermostat.

Ok I really need a thermostat asap, but I'm really worried about buying one of the cheaper ones and it being way off. I'll be using a Exo Terra Heat Wave Desert ( 16 watts) and I'll just be heating a single 29 gallon glass aquarium.Would it be safe to get a hydrofarm or should I just open my wallet and get a herpstat or helix? Again, I'm only looking to heat one cage.

Hydrofarm will work for you, I heat a couple racks with them

There is a lot of room for debate here. I personally use Hydrofarm, Johnsons, and Herpstat (all three currently) and I don't have too many complaints. For $26 the Hydrofarm does the job, my only issue is I don't know the life span of the probe, but once it's dead the whole unit has to be replaced. The Herpstat is definitely my favorite, and the Johnsons works well and I feel it is safe, but I could do without the fluctuations of the on/off thermostats but they are only within a couple degrees so it's not too bad. I say if you have the money, might as well go for quality. If you are really strapped the Hydrofarm works okay too but probably doesn't last as long as the other units. I want to try out the RBI VE-100, I think it's like $100 with shipping, not really sure though. Good luck!

Hydrofarm...six months, 21 tubs, zero problems. Can't beat it dollar for dollar

I got it today and trying to get it set right. Do you put your probes from the stat/thermometer under the substrate and on top the glass, or just on top of the substrate?

I put mine directly on my flexwatt.

Tape it directly on the flexwatt with clear tape not aluminum tape and monitor your temps for a while to see what minor adjustments you need to make.

The glass will 'buffer' the snake from the spikes that occure with all on/off t-stats. They work reasonable well with heavy enclosures and well not directly heating light weights but are not very safe with direct heat on a light weight system (heat source attached to a plastic tub, the spikes can be higher than expected) Glass should be fine, I'd re-think that T-stat if you chose to switch to tubs at a later date.

Alright, thanks a lot. And just to be sure, you mean tape it to the bottom of the heat pad right? Not between the pad and cage? Also the thermometer probe should be on or under the substrate?

There is a little debate on that. You can do both, the most accurate is in the enclosure on the bottom, but it is potentially unsafe as well. The probe MUST NOT MOVE (no tape inside either hot melt glue works well for this, big blobs ) if you are doing a interior mount. The other issue is pee/poo on the probe can cause a temporary over heating. If you go this route I'd usually suggest a back up, a second t-stat on/off with one plugged into the other and the second's probe on the heat source set to hotter than is required to reach 90 interior temps, if in the event of the above the second will shut down the first on before critical temps are reached.

The probe between the heat and glass will vary based on the room temps and glass temps. It is hard to get balance and often needs a bit more adjustment especially if the room varies in temperature. If it changes a lot and large swings the temps can change a lot too and again the same condition can occur IE in a 60º room the pad is set to 110ºF to get 90 interior, if the sun comes in during the day and the room shoots up to say 75º the glass of the aquarium warms up and the next thing you know the interior is reaching 105º. Again a second t-stat will stop this.

I am sure you will get lots of do this or do that, the answer is what kind of conditions you have and which one will produce safe consistent temps. If your room varies a lot I'd go inside, fixed really well on the bottom and place something over it to prevent faeces on the probe like a bit of tile. If will cause a bit of a buffer in that spot but it is localized and not where the hide is. The other consideration in this type of set up is the probe accuracy the on/off ones typically have a potential 2ºF error up or down due to this I'd never set it higher than 91 and likely stick to 90º

You will have to figure out what will work the best in your situation. No one can tell you what will work the best for you as they are not there and do not have enough information to have an informed decision.