If you want to do it yourself and deal directly with the auditor then you wouldn't need to use software compatible with that used by accountants. This is because auditors are content to work from printed documents. Being a control freak, I create my own financial statements for my SMSF, and make my own tax calculations and return, using Excel spreadsheets. These are available from my site below.The other option is to do it yourself and then deal with the auditor yourself. You could use something like Bgl Simple fund (most accountants I know use this anyway) as it has a trustee edition.
Cost first year $649 + $660 audit (based what I charge for your fund due to the number of investments)= $1,309.00 .. the next year $1,091
Obviously this is only advisable for people with the confidence to do this and who are willing to understand the applicable tax concepts and rules (from the comprehensive help file). Also for those willing to take responsibility for the accuracy of the data which they put in the spreadsheets and the accuracy of the financial statement and the return.
The spreadsheets can be used in single member or multi-member funds, and can handle foreign currencies. They are only for funds in accumulation phase investing only in financial investments such as bank deposits, shares, unit trusts, and managed funds. They can be adapted to suit other types of funds or investments. The 2013 version is coming out soon, alternatively the 2012 can be used and adapted for the 2013 tax return.