Bass boost isn't a gimmick, it's a tool/feature. It's used to boost the fequency output of a certain range, like Bullion said usually around 45Hz. You can get some amps or amp modules, as well as equalizers that can actually vary that frequency as well, giving you more control over where your bass is strongest and allowing you to tune your system more effectively.
Trying to drive any speaker hard when it's underpowered will inevitably kill it, as will overpowering it.
Neat install, dude. Looks the goods
Are the subs separated in the box? I know it's a bit late now, but it's usually a lot better if they are. A little bit of some sort of padding also helps the sound of the subs to be a bit more natural and a bit less 'bang' and a bit more 'thud'. Just a tip for DIY, as most pre-fab boxes come with.
Don't know if you've tried it, and haven't had a lot of personal experience with Alpine subs, but you might like to try just having the one sub on the amp and see how much you get out of it/how it sounds, as the amp's pretty underpowered for the job. You'd probably find it would go louder easier, and may or may not find it to sound a bit better. Just a thought anyway. Had 2 subs in my last setup and I just kept playing around seeing what things sounded like etc. All good fun
Sounds like you have the wiring sorted, subs are in series (taking them to 4 ohms each) and then in paralell on the amp (back down to 2 ohms). Could also do the reverse, but as long as it works, all is well
Did you find it difficult to make the box/what did you find the hardest? I'm eventually looking at a custom box. VR4 boot is just too shallow.