"Appropriate time" is either quarterly, or after filing your Australian Tax Return and receiving the demand notice from the ATO.
Once the first income tax return is lodged, you will subsequently be required to make quarterly PAYG instalment payments. These amounts will be credited against your next year’s tax return.
So, income tax is calculated on salary + HDP.
In terms of salary, you are able to claim certain allowable deductions (eg, professional or union memberships, licence renewal and related medical examination costs, technical publications, etc). If you have a non-working wife you may be able to claim dependent spouse tax offsets, etc.
I think you're right that you are limited to $50-100K per annum salary sacrifice into super
Theoretically there is no limit on amounts that can be contributed to superannuation, but if you want concessional tax treatment, then the 2008 limit for employer contributions (including salary-packaged amounts) is $50,000. If you’re contributing yourself (ie, personal contributions) and not claiming a deduction for that amount, (employee pilots can't anyway), then the cap is $150,000.
I am in the process of setting up a custom fund and will then offset franking credits etc against the 15% tax
All superannuation funds will utilise franking credits to their advantage. A DIY self-managed superannuation fund can be effective but get good advice before doing it. Annual accounting, tax, audit and statutory fees can be high so you need a decent amount in it to make it worthwhile.
Older pilots should look at the new 'transition to retirement' rules that kicked in last year. After age 55 they can start to draw down a pension that may be concessionally taxed (ie, 15% off their marginal tax rate). At age 60 the amounts may be tax-free.
Rgds
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