ilr(o) time outside Uk

[dhana]

I had come to the UK in 2005 on HSMP visa. I understand I can apply under HSMP-JR however I realised I have spent about 9.5 months outside UK.
None of the stay is above 3 months and in most cases the period spend outside is just 3 days. However it looks like I was only coming here for the weekend over the last 9 months.
Further during this period I was paid from an overseas company and hence was self employed.
I don't know if this will affect my application and how I should put this in my application.
Would it be better to apply by post or by taking an appointment so I can possibly explain them and also I might be required to travel so need access to my passport
I would be very appreciative if someone with similiar history guide me.
Thanks.