First thing: encrypt that Dedicated server's entire hard drive.
Secondly: encrypt that wallet.dat file
Thirdly: use EVERY possible method of attack defense you can. Use googleauth for 2 step log in. disable root access. If you must run SSH, run it under a random port. NOT port 22. use tripwire mod_sec/mod_evasive, if you think it might be good... add it. use UFW firewall. Use insane settings. If you only plan to sell to one country: block ALL IP's that are not within that country
Disable ALL error notifications and disable any information that may allow the attacker to gain any information about what the server is run on (no "this server run on apache centos" etc). I do assume you do know this, but im just giving fair warning.
Host as few applications beyond the bare minimum. (so no minecraft servers).
I personally recommend not keeping funds in a hot wallet because ~/.bitcoin/wallet.dat is the most searched for thing by hackers
Now... How can you have two different wallets on the same machine? well. there's a few ways to do it... If you want to keep generating infinite new addresses (using infinite seeds) all the time and have a good contingency plan in place for your wallet.dat file (like hourly back up etc), you could run 2 instances of bitcoind. (commandline version is what you want for this) Two instances can be run by changing the listening ports on one of the two bitcoind instances and running each instance on its own user account. you can then (depending on which user you are paying to) have php connect to the respective bitcoin client and request an address for payment.
Another idea i would propose could be using one bitcoin client and having accounts. If you are okay sharing one wallet and one daemon, but need your own account for accounting balances, its a breeze
there are a few projects that actually are pretty good. I started writing a basic bitcoin escrow system based off of my own coding and using "The Bitcoin Shopping Cart Interface package" and "The Bitcoin Shopping Cart Interface package"
I use to have a much more advance version i built for FreiCoin but the wonderful people over at FDCServers destroyed my development server on me (thanks guys). So I am pretty far behind again. However you should at least have an idea of maybe a general direction to start
This version requires no bitcoind at all which is pretty unique. But if you want a wallet, then you may need to integrate that yourself.
you could also consider installing drupal and modifying the source to have a two different plug ins going to the two different daemons.
there are many options.
you can even start from scratch, good documentation is available here.
Please let me know if this was useful or not, and let me know if there is further clarification needed. If you want to truly have your own page it's a lot of work...
Also, check out https://github.com/Bit-Wasp/BitWasp
I have been playing around with it and its been pretty cool so far.
thanks for giving me the information i needed to try and respond as best i can