I want to invest some of my self-managed super funds into two starts ups? Do I have to set up another smsf to do so, anything else I need to be aware of?

If you want to invest in two start-ups, I presume that they are unrelated, and so will be separate assets, so on the face of things, should pose no problem.
BUT
dont do it!!! despite the fact that there is no legal reason not to do this in a SMSF, there is a can of whoop-ass waiting for you if you do. There are issues such as control, part 8 associates, in-house assets, sole purpose tests, audit valuation of the assets which could affect transfer balance caps, pension consequences, etc etc etc.

It is seriously a minefield and you seriously need to be all over the SIS rules and regs to contemplate this. (And to be honest, if you were all over the SIS rules and regs, you wouldnt be here).

I have a SMSF, I am a registered SMSF auditor and Chartered Accountant, and I would not do this in a pink fit!
You are begging the ATO to audit your fund each and every year. You are also going to pay for your SMSF auditor's kids school fees every year.....because as a SMSF auditor I would refuse the job. Which means that the only auditors willing to take this sort of work charge like wounded bulls!!

LENDING to a company (unrelated) is a different story though: you CAN do this, and as long as you can dempnstrate you have considered the risks and tick all the boxes with the auditor, then you should not have too many headaches......

good luck
bc